Who is Who in Phylogenetic Networks (Réseaux Phylogénétiques, Phylogenetische Netzwerke, Redes Filogenéticas, Xarxes Filogenètiques, 演化網路, شبکه فیلوژنتیک)

All publications ( Html | Bibtex | Both ) Order by: Type | Year

2020

1

Katharina Huber and Guillaume Scholz. Phylogenetic networks that are their own fold-ups. In AAM, Vol. 113(101959):1-24, 2020.
Keywords: characterization, explicit network, FU-stable network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1804.01841.

@Article{HuberScholz2020,
AUTHOR = {Huber, Katharina and Scholz, Guillaume},
TITLE = {Phylogenetic networks that are their own fold-ups},
YEAR = {2020},
JOURNAL = {AAM},
VOLUME = {113},
NUMBER = {101959},
PAGES = {1-24},
URL = {https://doi.org/10.1016/j.aam.2019.101959},
NOTE = {https://arxiv.org/abs/1804.01841},
KEYWORDS = {characterization, explicit network, FU-stable network, phylogenetic network, phylogeny}
}

2

Andrew R. Francis, Daniel H. Huson and Mike Steel. Normalising phylogenetic networks. 2020.
Keywords: explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network.
Note: https://arxiv.org/abs/2008.07797.

@Misc{FHS2020,
AUTHOR = {Francis, Andrew R. and Huson, Daniel H. and Steel, Mike},
TITLE = {Normalising phylogenetic networks},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2008.07797},
KEYWORDS = {explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network}
}

3

Gabriel Cardona and Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020.
Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.

@Article{CardonaZhang2020,
AUTHOR = {Cardona, Gabriel and Zhang, Louxin},
TITLE = {Counting and Enumerating Tree-Child Networks and Their Subclasses},
YEAR = {2020},
JOURNAL = {JCSS},
VOLUME = {114},
PAGES = {84-104},
URL = {https://doi.org/10.1016/j.jcss.2020.06.001},
KEYWORDS = {counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network}
}

4

Michael Fuchs, Guan-Ru Yu and Louxin Zhang. On the Asymptotic Growth of the Number of Tree-Child Networks. 2020.
Keywords: counting, explicit network, phylogenetic network, phylogeny, tree-child network.
Note: https://arxiv.org/abs/2003.08049.

@Misc{FRY2020,
AUTHOR = {Fuchs, Michael and Yu, Guan-Ru and Zhang, Louxin},
TITLE = {On the Asymptotic Growth of the Number of Tree-Child Networks},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2003.08049},
KEYWORDS = {counting, explicit network, phylogenetic network, phylogeny, tree-child network}
}

5

Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:22-27 of LNCS, Springer, 2020.
Keywords: cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network.

@InProceedings{Zhang2020,
AUTHOR = {Zhang, Louxin},
TITLE = {Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks},
YEAR = {2020},
BOOKTITLE = {WALCOM20},
VOLUME = {12049},
PAGES = {22-27},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-39881-1_3},
KEYWORDS = {cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network}
}

6

Andreas Gunawan, Jeyaram Rathin and Louxin Zhang. Counting and enumerating galled networks. In DAM, Vol. 283:644-654, 2020.
Keywords: counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1812.08569.

@Article{GRZ2020,
AUTHOR = {Gunawan, Andreas and Rathin, Jeyaram and Zhang, Louxin},
TITLE = {Counting and enumerating galled networks},
YEAR = {2020},
JOURNAL = {DAM},
VOLUME = {283},
PAGES = {644-654},
URL = {https://doi.org/10.1016/j.dam.2020.03.005},
NOTE = {https://arxiv.org/abs/1812.08569},
KEYWORDS = {counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny}
}

7

Marefatollah Mansouri. Counting General Phylogenetic networks. 2020.
Keywords: counting, explicit network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/2005.14547.

@Misc{Mansouri2020b,
AUTHOR = {Mansouri, Marefatollah},
TITLE = {Counting General Phylogenetic networks},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2005.14547},
KEYWORDS = {counting, explicit network, phylogenetic network, phylogeny}
}

8

Marefatollah Mansouri. Combinatorial properties of phylogenetic networks. PhD thesis, Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry, 2020.
Keywords: counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny.
Note: https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf.

@PhdThesis{Mansouri2020,
AUTHOR = {Mansouri, Marefatollah},
TITLE = {Combinatorial properties of phylogenetic networks},
YEAR = {2020},
SCHOOL = {Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry},
NOTE = {https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf},
KEYWORDS = {counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny}
}

9

Mathilde Bouvel, Philippe Gambette and Marefatollah Mansouri. Counting Phylogenetic Networks of Level 1 and 2. In JOMB, 2020.
Keywords: counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1909.10460, to appear.

@Article{BGM2020,
AUTHOR = {Bouvel, Mathilde and Gambette, Philippe and Mansouri, Marefatollah},
TITLE = {Counting Phylogenetic Networks of Level 1 and 2},
YEAR = {2020},
JOURNAL = {JOMB},
NOTE = {https://arxiv.org/abs/1909.10460, to appear},
KEYWORDS = {counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny}
}

10

Jonathan Klawitter and Peter Stumpf. Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings. 2020.
Keywords: explicit network, FPT, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, visualization.
Note: https://arxiv.org/abs/2008.08960.

@Misc{KlawitterStumpf2020,
AUTHOR = {Klawitter, Jonathan and Stumpf, Peter},
TITLE = {Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2008.08960},
KEYWORDS = {explicit network, FPT, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, visualization}
}

11

Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long and Yukihiro Murakami. Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes. 2020.
Keywords: characterization, distinguishability, explicit network, galled tree, phylogenetic network, population genetics, semidirected network, statistical model, uniqueness.
Note: https://arxiv.org/abs/2007.08782.

@Misc{GIJJLM2020,
AUTHOR = {Gross, Elizabeth and van Iersel, Leo and Janssen, Remie and Jones, Mark and Long, Colby and Murakami, Yukihiro},
TITLE = {Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2007.08782},
KEYWORDS = {characterization, distinguishability, explicit network, galled tree, phylogenetic network, population genetics, semidirected network, statistical model, uniqueness}
}

12

Remie Janssen, Mark Jones and Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences. In AlCoB20, Vol. 12099:77-92 of LNCS, Springer, 2020.
Keywords: cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network.

@InProceedings{JJY2020,
AUTHOR = {Janssen, Remie and Jones, Mark and Murakami, Yukihiro},
TITLE = {Combining Networks Using Cherry Picking Sequences},
YEAR = {2020},
BOOKTITLE = {AlCoB20},
VOLUME = {12099},
PAGES = {77-92},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-42266-0_7},
KEYWORDS = {cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network}
}

13

Hannah Brown, Lei Zuo and Dan Gusfield. Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. In AlCoB2020, Vol. 12099:63-76 of LNCS, Springer, 2020.
Keywords: from binary characters, History bound, integer linear programming, minimum number, phylogeny, SAT.
Note: https://doi.org/10.1007/978-3-030-42266-0_6.

@InProceedings{BZG2020,
AUTHOR = {Brown, Hannah and Zuo, Lei and Gusfield, Dan},
TITLE = {Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology},
YEAR = {2020},
BOOKTITLE = {AlCoB2020},
VOLUME = {12099},
PAGES = {63-76},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-42266-0_6},
NOTE = {https://doi.org/10.1007/978-3-030-42266-0_6},
KEYWORDS = {from binary characters, History bound, integer linear programming, minimum number, phylogeny, SAT}
}

14

Remie Janssen and Yukihiro Murakami. Linear Time Algorithm for Tree-Child Network Containment. In AlCoB20, Vol. 12099:93-107 of LNCS, Springer, 2020.
Keywords: explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence.
Note: https://doi.org/10.1007/978-3-030-42266-0_8.

@InProceedings{JanssenMurakami2020,
AUTHOR = {Janssen, Remie and Murakami, Yukihiro},
TITLE = {Linear Time Algorithm for Tree-Child Network Containment},
YEAR = {2020},
BOOKTITLE = {AlCoB20},
VOLUME = {12099},
PAGES = {93-107},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-42266-0_8},
NOTE = {https://doi.org/10.1007/978-3-030-42266-0_8},
KEYWORDS = {explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence}
}

15

Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation. In TCBB, Vol. 17(1):14-26, 2020.
Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf.

@Article{IJJMZ,
AUTHOR = {van Iersel, Leo and Janssen, Remie and Jones, Mark and Murakami, Yukihiro and Zeh, Norbert},
TITLE = {Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation},
YEAR = {2020},
JOURNAL = {TCBB},
VOLUME = {17},
NUMBER = {1},
PAGES = {14-26},
URL = {https://doi.org/10.1109/TCBB.2019.2934957},
NOTE = {http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf},
KEYWORDS = {hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction, weakly displaying}
}

16

Momoko Hayamizu, Katharina Huber, Vincent Moulton and Yukihiro Murakami. Recognizing and realizing cactus metrics. In IPL, Vol. 157(105916):1-5, 2020.
Keywords: cactus graph, from distances, level k phylogenetic network, optimal realization, polynomial.
Note: https://doi.org/10.1016/j.ipl.2020.105916.

@Article{HHMM2020,
AUTHOR = {Hayamizu, Momoko and Huber, Katharina and Moulton, Vincent and Murakami, Yukihiro},
TITLE = {Recognizing and realizing cactus metrics},
YEAR = {2020},
JOURNAL = {IPL},
VOLUME = {157},
NUMBER = {105916},
PAGES = {1-5},
URL = {https://doi.org/10.1016/j.ipl.2020.105916},
NOTE = {https://doi.org/10.1016/j.ipl.2020.105916},
KEYWORDS = {cactus graph, from distances, level k phylogenetic network, optimal realization, polynomial}
}

17

Leo van Iersel, Vincent Moulton and Yukihiro Murakami. Reconstructibility of unrooted level-k phylogenetic networks from distances. In AAM, Vol. 120(102075):1-30, 2020.
Keywords: from distances, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1016/j.aam.2020.102075.

@Article{IMM2020,
AUTHOR = {van Iersel, Leo and Moulton, Vincent and Murakami, Yukihiro},
TITLE = {Reconstructibility of unrooted level-k phylogenetic networks from distances},
YEAR = {2020},
JOURNAL = {AAM},
VOLUME = {120},
NUMBER = {102075},
PAGES = {1-30},
URL = {https://doi.org/10.1016/j.aam.2020.102075},
NOTE = {https://doi.org/10.1016/j.aam.2020.102075},
KEYWORDS = {from distances, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

18

Jonathan Klawitter. The agreement distance of unrooted phylogenetic networks. In DMTCS, Vol. 21(2):22.1-23, 2020.
Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny.
Note: https://dmtcs.episciences.org/6567/pdf.

@Article{Klawitter2020b,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The agreement distance of unrooted phylogenetic networks},
YEAR = {2020},
JOURNAL = {DMTCS},
VOLUME = {21},
NUMBER = {2},
PAGES = {22.1-23},
URL = {https://doi.org/10.23638/DMTCS-22-1-22},
NOTE = {https://dmtcs.episciences.org/6567/pdf},
KEYWORDS = {agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny}
}

19

Stefan Forcey and Drew Scalzo. Phylogenetic networks as circuits with resistance distance. 2020.
Keywords: circular split system, from distances, level k phylogenetic network, NeighborNet, nested network, phylogenetic network, phylogeny, split network.
Note: https://arxiv.org/abs/2007.13574.

@Misc{ForceyScalzo2020,
AUTHOR = {Forcey, Stefan and Scalzo, Drew},
TITLE = {Phylogenetic networks as circuits with resistance distance},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2007.13574},
KEYWORDS = {circular split system, from distances, level k phylogenetic network, NeighborNet, nested network, phylogenetic network, phylogeny, split network}
}

20

Cassandra Durell and Stefan Forcey. Level-1 phylogenetic networks and their balanced minimum evolution polytopes. In JOMB, Vol. 80:1235-1263, 2020.
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/pdf/1905.09160.pdf.

@Article{DurellForcey2020,
AUTHOR = {Durell, Cassandra and Forcey, Stefan},
TITLE = {Level-1 phylogenetic networks and their balanced minimum evolution polytopes},
YEAR = {2020},
JOURNAL = {JOMB},
VOLUME = {80},
PAGES = {1235-1263},
URL = {https://doi.org/10.1007/s00285-019-01458-w},
NOTE = {https://arxiv.org/pdf/1905.09160.pdf},
KEYWORDS = {from distances, galled tree, phylogenetic network, phylogeny, reconstruction, split network}
}

21

Stefan Forcey and Drew Scalzo. Galois connections for phylogenetic networks and their polytopes. 2020.
Keywords: characterization, from distances, galled tree, planar, reconstruction, split network.
Note: https://arxiv.org/abs/2004.11944.

@Misc{ForceyScalzo2020b,
AUTHOR = {Forcey, Stefan and Scalzo, Drew},
TITLE = {Galois connections for phylogenetic networks and their polytopes},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2004.11944},
KEYWORDS = {characterization, from distances, galled tree, planar, reconstruction, split network}
}

22

Simone Linz and Charles Semple. Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks. In JOMB, 2020.
Keywords: explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/2002.00483, to appear.

@Article{LinzSemple2020,
AUTHOR = {Linz, Simone and Semple, Charles},
TITLE = {Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks},
YEAR = {2020},
JOURNAL = {JOMB},
URL = {https://doi.org/10.1007/s00285-020-01533-7},
NOTE = {https://arxiv.org/abs/2002.00483, to appear},
KEYWORDS = {explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

23

Hadi Poormohammadi and Mohsen Sardari Zarchi. Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets. In PLoS ONE, Vol. 15(9):e0227842.1-25, 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1371/journal.pone.0227842.

@Article{PoormohammadiSardariZarchi2020,
AUTHOR = {Poormohammadi, Hadi and Sardari Zarchi, Mohsen},
TITLE = {Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets},
YEAR = {2020},
JOURNAL = {PLoS ONE},
VOLUME = {15},
NUMBER = {9},
PAGES = {e0227842.1-25},
URL = {https://doi.org/10.1371/journal.pone.0227842},
NOTE = {https://doi.org/10.1371/journal.pone.0227842},
KEYWORDS = {explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction}
}

24

Hadi Poormohammadi, Mohsen Sardari Zarchi and Hossein Ghaneai. NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization. In JTB, Vol. 489(110144), 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1016/j.jtbi.2019.110144.

@Article{PSG2020,
AUTHOR = {Poormohammadi, Hadi and Sardari Zarchi, Mohsen and Ghaneai, Hossein},
TITLE = {NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization},
YEAR = {2020},
JOURNAL = {JTB},
VOLUME = {489},
NUMBER = {110144},
URL = {https://doi.org/10.1016/j.jtbi.2019.110144},
NOTE = {https://doi.org/10.1016/j.jtbi.2019.110144},
KEYWORDS = {explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction}
}

25

Katharina Huber, Simone Linz and Vincent Moulton. Weakly displaying trees in temporal tree-child network. 2020.
Keywords: cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying.
Note: https://arxiv.org/abs/2004.02634.

@Misc{HLM2020,
AUTHOR = {Huber, Katharina and Linz, Simone and Moulton, Vincent},
TITLE = {Weakly displaying trees in temporal tree-child network},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2004.02634},
KEYWORDS = {cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying}
}

26

Joan Carles Pons, Celine Scornavacca and Gabriel Cardona. Generation of Level-k LGT Networks. In TCBB, Vol. 17(1):158-164, 2020.
Keywords: explicit network, level k phylogenetic network, LGT network, phylogenetic network, phylogeny.

@Article{PSC2020,
AUTHOR = {Pons, Joan Carles and Scornavacca, Celine and Cardona, Gabriel},
TITLE = {Generation of Level-k LGT Networks},
YEAR = {2020},
JOURNAL = {TCBB},
VOLUME = {17},
NUMBER = {1},
PAGES = {158-164},
URL = {https://doi.org/10.1109/TCBB.2019.2895344},
KEYWORDS = {explicit network, level k phylogenetic network, LGT network, phylogenetic network, phylogeny}
}

2019

1

Steven Kelk, Fabio Pardi, Celine Scornavacca and Leo van Iersel. Finding the most parsimonious or likely tree in a network with respect to an alignment. In JOMB, Vol. 78:527-547, 2019.
Keywords: APX hard, from network, from sequences, likelihood, NP complete, parsimony.
Note: https://arxiv.org/abs/1707.03648.

@Article{KPSI2019,
AUTHOR = {Kelk, Steven and Pardi, Fabio and Scornavacca, Celine and van Iersel, Leo},
TITLE = {Finding the most parsimonious or likely tree in a network with respect to an alignment},
YEAR = {2019},
JOURNAL = {JOMB},
VOLUME = {78},
PAGES = {527-547},
URL = {http://dx.doi.org/10.1007/s00285-018-1282-2},
NOTE = {https://arxiv.org/abs/1707.03648},
KEYWORDS = {APX hard, from network, from sequences, likelihood, NP complete, parsimony}
}

2

Joan Carles Pons, Charles Semple and Mike Steel. Tree-based networks: characterisations, metrics, and support trees. In JOMB, Vol. 78(4):899-918, 2019.
Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1710.07836.

@Article{PSS2019,
AUTHOR = {Pons, Joan Carles and Semple, Charles and Steel, Mike},
TITLE = {Tree-based networks: characterisations, metrics, and support trees},
YEAR = {2019},
JOURNAL = {JOMB},
VOLUME = {78},
NUMBER = {4},
PAGES = {899-918},
URL = {https://doi.org/10.1007/s00285-018-1296-9},
NOTE = {https://arxiv.org/abs/1710.07836},
KEYWORDS = {characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network}
}

3

Katharina Huber, Vincent Moulton and Taoyang Wu. Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. In JOC, Vol. 36:200-231, 2019.
Keywords: characterization, explicit network, phylogenetic network, phylogeny.
Note: https://link.springer.com/content/pdf/10.1007/s00357-018-9279-5.pdf.

@Article{HMW2019,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks},
YEAR = {2019},
JOURNAL = {JOC},
VOLUME = {36},
PAGES = {200-231},
NOTE = {https://link.springer.com/content/pdf/10.1007/s00357-018-9279-5.pdf},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny}
}

4

Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. In AAM, Vol. 105:102-129, 2019.
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: https://doi.org/10.1016/j.aam.2019.01.004.

@Article{LinzSemple2019,
AUTHOR = {Linz, Simone and Semple, Charles},
TITLE = {Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies},
YEAR = {2019},
JOURNAL = {AAM},
VOLUME = {105},
PAGES = {102-129},
URL = {https://doi.org/10.1016/j.aam.2019.01.004},
NOTE = {https://doi.org/10.1016/j.aam.2019.01.004},
KEYWORDS = {agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

5

Jonathan Klawitter. The agreement distance of rooted phylogenetic networks. In DMTCS, Vol. 21(3):19.1-24, 2019.
Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1806.05800.

@Article{Klawitter2019b,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The agreement distance of rooted phylogenetic networks},
YEAR = {2019},
JOURNAL = {DMTCS},
VOLUME = {21},
NUMBER = {3},
PAGES = {19.1-24},
URL = {https://doi.org/10.23638/DMTCS-21-3-19},
NOTE = {https://arxiv.org/abs/1806.05800},
KEYWORDS = {agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny, SPR distance}
}

6

Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. In DAM, Vol. 260:131-143, 2019.
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.02965.

@Article{DIKL2019,
AUTHOR = {D{\~A}�cker, Janosch and van Iersel, Leo and Kelk, Steven and Linz, Simone},
TITLE = {Deciding the existence of a cherry-picking sequence is hard on two trees},
YEAR = {2019},
JOURNAL = {DAM},
VOLUME = {260},
PAGES = {131-143},
URL = {https://doi.org/10.1016/j.dam.2019.01.031},
NOTE = {https://arxiv.org/abs/1712.02965},
KEYWORDS = {cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network}
}

7

Jonathan Klawitter and Simone Linz. On the Subnet Prune and Regraft Distance. In ELJC, Vol. 26(2):P2.3.1-23, 2019.
Keywords: agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://arxiv.org/abs/1805.07839.

@Article{KlawitterLinz2019,
AUTHOR = {Klawitter, Jonathan and Linz, Simone},
TITLE = {On the Subnet Prune and Regraft Distance},
YEAR = {2019},
JOURNAL = {ELJC},
VOLUME = {26},
NUMBER = {2},
PAGES = {P2.3.1-23},
URL = {https://doi.org/10.37236/7860},
NOTE = {https://arxiv.org/abs/1805.07839},
KEYWORDS = {agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network}
}

8

Michael Fuchs, Bernhard Gittenberger and Marefatollah Mansouri. Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks. In Australasian Journal of Combinatorics, Vol. 73(2):385-423, 2019.
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1803.11325, see also erratum at https://arxiv.org/abs/2006.15784.

@Article{FGM2019,
AUTHOR = {Fuchs, Michael and Gittenberger, Bernhard and Mansouri, Marefatollah},
TITLE = {Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks},
YEAR = {2019},
JOURNAL = {Australasian Journal of Combinatorics},
VOLUME = {73},
NUMBER = {2},
PAGES = {385-423},
NOTE = {https://arxiv.org/abs/1803.11325, see also erratum at https://arxiv.org/abs/2006.15784},
KEYWORDS = {counting, explicit network, normal network, phylogenetic network, phylogeny}
}

9

Andreas Gunawan, Hongwei Yan and Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network.
Note: https://arxiv.org/abs/1806.07625.

@Article{GYZ2019,
AUTHOR = {Gunawan, Andreas and Yan, Hongwei and Zhang, Louxin},
TITLE = {Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem},
YEAR = {2019},
JOURNAL = {JCB},
VOLUME = {25},
NUMBER = {3},
URL = {https://doi.org/10.1089/cmb.2018.0220},
NOTE = {https://arxiv.org/abs/1806.07625},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network}
}

10

R. A. Leo Elworth, Huw A. Ogilvie, Jiafan Zhu and Luay Nakhleh. Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29 of Computational Biology, Springer, 2019.
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey.
Note: https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf

@InBook{EOZN2019,
AUTHOR = {Elworth, R. A. Leo and Ogilvie, Huw A. and Zhu, Jiafan and Nakhleh, Luay},
TITLE = {Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization},
YEAR = {2019},
BOOKTITLE = {Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret},
VOLUME = {29},
EDITOR = {Warnow, Tandy},
SERIES = {Computational Biology},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-10837-3_13},
NOTE = {https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf KEYWORDS = {explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey}
}

11

Louxin Zhang. Clusters, Trees, and Phylogenetic Network Classes. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29:277-315 of Computational Biology, Springer, 2019.
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment.

@InBook{Zhang2019,
AUTHOR = {Zhang, Louxin},
TITLE = {Clusters, Trees, and Phylogenetic Network Classes},
YEAR = {2019},
BOOKTITLE = {Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret},
VOLUME = {29},
PAGES = {277-315},
EDITOR = {Warnow, Tandy},
SERIES = {Computational Biology},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-10837-3_12},
KEYWORDS = {cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment}
}

12

Louxin Zhang. Generating normal networks via leaf insertion and nearest neighbor interchange. In BMC Bioinformatics, Vol. 20(642):1-9, 2019.
Keywords: enumeration, explicit network, generation, NNI moves, phylogenetic network, phylogeny.
Note: https://link.springer.com/content/pdf/10.1186/s12859-019-3209-3.pdf.

@Article{Zhang2019b,
AUTHOR = {Zhang, Louxin},
TITLE = {Generating normal networks via leaf insertion and nearest neighbor interchange},
YEAR = {2019},
JOURNAL = {BMC Bioinformatics},
VOLUME = {20},
NUMBER = {642},
PAGES = {1-9},
URL = {https://doi.org/10.1186/s12859-019-3209-3},
NOTE = {https://link.springer.com/content/pdf/10.1186/s12859-019-3209-3.pdf},
KEYWORDS = {enumeration, explicit network, generation, NNI moves, phylogenetic network, phylogeny}
}

13

Juan Wang and Maozu Guo. IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs. In ICNC-FSKD19, Vol. 1075:894-900 of Advances in Intelligent Systems and Computing, Springer, 2019.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program IGNet, Program LNetwork, reconstruction, software.

@InProceedings{WangGuo2019,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs},
YEAR = {2019},
BOOKTITLE = {ICNC-FSKD19},
VOLUME = {1075},
PAGES = {894-900},
SERIES = {Advances in Intelligent Systems and Computing},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-32591-6_97},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program IGNet, Program LNetwork, reconstruction, software}
}

14

Yukihiro Murakami, Leo van Iersel, Remie Janssen, Mark Jones and Vincent Moulton. Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks. In BMB, Vol. 81:3823-3863, 2019.
Keywords: from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, tree-child network, uniqueness, valid network.
Note: https://doi.org/10.1007/s11538-019-00641-w.

@Article{MIJJM,
AUTHOR = {Murakami, Yukihiro and van Iersel, Leo and Janssen, Remie and Jones, Mark and Moulton, Vincent},
TITLE = {Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks},
YEAR = {2019},
JOURNAL = {BMB},
VOLUME = {81},
PAGES = {3823-3863},
URL = {https://doi.org/10.1007/s11538-019-00641-w},
NOTE = {https://doi.org/10.1007/s11538-019-00641-w},
KEYWORDS = {from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, tree-child network, uniqueness, valid network}
}

15

Yan Hong and Juan Wang. Frin: An Efficient Method for Representing Genome Evolutionary History. In Frontiers in Genetics, Vol. 10(1261):1-8, 2019.
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program Frin, reconstruction.
Note: https://doi.org/10.3389/fgene.2019.01261.

@Article{HongWang2019,
AUTHOR = {Hong, Yan and Wang, Juan},
TITLE = {Frin: An Efficient Method for Representing Genome Evolutionary History},
YEAR = {2019},
JOURNAL = {Frontiers in Genetics},
VOLUME = {10},
NUMBER = {1261},
PAGES = {1-8},
URL = {https://doi.org/10.3389/fgene.2019.01261},
NOTE = {https://doi.org/10.3389/fgene.2019.01261},
KEYWORDS = {explicit network, from clusters, phylogenetic network, phylogeny, Program Frin, reconstruction}
}

16

Juan Wang and Maozu Guo. A review of metrics measuring dissimilarity for rooted phylogenetic networks. In Briefings in Bioinformatics, Vol. 20(6):1972-1980, 2019.
Keywords: distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network.

@Article{WangGuo2019b,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {A review of metrics measuring dissimilarity for rooted phylogenetic networks},
YEAR = {2019},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {20},
NUMBER = {6},
PAGES = {1972-1980},
URL = {https://doi.org/10.1093/bib/bby062},
KEYWORDS = {distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network}
}

17

Christopher Blair and Cécile Ané. Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. In SB, Vol. 69(3):593-601, 2019.
Keywords: likelihood, phylogenetic network, phylogeny, Program PhyloNetwork, Program PhyloNetworks SNaQ, survey.

@Article{BlairAne2019,
AUTHOR = {Blair, Christopher and An{\~A}�, C{\~A}�cile},
TITLE = {Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data},
YEAR = {2019},
JOURNAL = {SB},
VOLUME = {69},
NUMBER = {3},
PAGES = {593-601},
URL = {https://doi.org/10.1093/sysbio/syz056},
KEYWORDS = {likelihood, phylogenetic network, phylogeny, Program PhyloNetwork, Program PhyloNetworks SNaQ, survey}
}

18

Péter L. Erdös, Leo van Iersel and Mark Jones. Not all phylogenetic networks are leaf-reconstructible. In JOMB, Vol. 79(5):1623-1638, 2019.
Keywords: from subnetworks, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1007/s00285-019-01405-9.

@Article{EIJ2019,
AUTHOR = {Erd{\~A}�s, P{\~A}�ter L. and van Iersel, Leo and Jones, Mark},
TITLE = {Not all phylogenetic networks are leaf-reconstructible},
YEAR = {2019},
JOURNAL = {JOMB},
VOLUME = {79},
NUMBER = {5},
PAGES = {1623-1638},
URL = {https://doi.org/10.1007/s00285-019-01405-9},
NOTE = {https://doi.org/10.1007/s00285-019-01405-9},
KEYWORDS = {from subnetworks, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

19

Konstantinos Mampentzidis. Comparison and Construction of Phylogenetic Trees and Networks. PhD thesis, Aarhus University, Denmark, 2019.
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf.

@PhdThesis{Mampentzidis2019,
AUTHOR = {Mampentzidis, Konstantinos},
TITLE = {Comparison and Construction of Phylogenetic Trees and Networks},
YEAR = {2019},
SCHOOL = {Aarhus University, Denmark},
URL = {https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf},
NOTE = {https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf},
KEYWORDS = {distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, triplet distance}
}

20

Jesper Jansson, Konstantinos Mampentzidis, Ramesh Rajaby and Wing-Kin Sung. Computing the Rooted Triplet Distance Between Phylogenetic Networks. In IWOCA19, Vol. 11638:290-303 of LNCS, Springer, 2019.
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, triplet distance.

@InProceedings{JMS2019,
AUTHOR = {Jansson, Jesper and Mampentzidis, Konstantinos and Rajaby, Ramesh and Sung, Wing-Kin},
TITLE = {Computing the Rooted Triplet Distance Between Phylogenetic Networks},
YEAR = {2019},
BOOKTITLE = {IWOCA19},
VOLUME = {11638},
PAGES = {290-303},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-25005-8_24},
KEYWORDS = {distance between networks, from network, phylogenetic network, phylogeny, polynomial, triplet distance}
}

21

Janosch Döcker, Simone Linz and Charles Semple. Displaying trees across two phylogenetic networks. In TCS, Vol. 796:129-146, 2019.
Keywords: display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1901.06612.

@Article{DLS2019,
AUTHOR = {D{\~A}�cker, Janosch and Linz, Simone and Semple, Charles},
TITLE = {Displaying trees across two phylogenetic networks},
YEAR = {2019},
JOURNAL = {TCS},
VOLUME = {796},
PAGES = {129-146},
URL = {https://doi.org/10.1016/j.tcs.2019.09.003},
NOTE = {https://arxiv.org/abs/1901.06612},
KEYWORDS = {display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network}
}

22

Katharina Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami and Charles Semple. Rooting for phylogenetic networks. 2019.
Keywords: explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network.
Note: https://arxiv.org/abs/1906.07430.

@Misc{HIJJMMS2019,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Janssen, Remie and Jones, Mark and Moulton, Vincent and Murakami, Yukihiro and Semple, Charles},
TITLE = {Rooting for phylogenetic networks},
YEAR = {2019},
NOTE = {https://arxiv.org/abs/1906.07430},
KEYWORDS = {explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network}
}

23

Gabriel Cardona, Joan Carles Pons and Celine Scornavacca. Generation of Binary Tree-Child phylogenetic networks. In PLoS Computational Biology, Vol. 15(10):e1007440.1-29, 2019.
Keywords: enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network.
Note: https://doi.org/10.1371/journal.pcbi.1007440.

@Article{CPS2019,
AUTHOR = {Cardona, Gabriel and Pons, Joan Carles and Scornavacca, Celine},
TITLE = {Generation of Binary Tree-Child phylogenetic networks},
YEAR = {2019},
JOURNAL = {PLoS Computational Biology},
VOLUME = {15},
NUMBER = {10},
PAGES = {e1007440.1-29},
URL = {https://doi.org/10.1371/journal.pcbi.1007440},
NOTE = {https://doi.org/10.1371/journal.pcbi.1007440},
KEYWORDS = {enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network}
}

2018

1

Leo van Iersel, Steven Kelk, Giorgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. In ALG, Vol. 80(11):2993-3022, 2018.
Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment.
Note: https://hal.inria.fr/hal-01599716.

@Article{IKSSB2018,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Stamoulis, Giorgios and Stougie, Leen and Boes, Olivier},
TITLE = {On unrooted and root-uncertain variants of several well-known phylogenetic network problems},
YEAR = {2018},
JOURNAL = {ALG},
VOLUME = {80},
NUMBER = {11},
PAGES = {2993-3022},
URL = {https://doi.org/10.1007/s00453-017-0366-5},
NOTE = {https://hal.inria.fr/hal-01599716},
KEYWORDS = {explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment}
}

2

Laura Jetten and Leo van Iersel. Nonbinary tree-based phylogenetic networks. In TCBB, Vol. 15(1):205-217, 2018.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1601.04974.

@Article{JettenIersel2018,
AUTHOR = {Jetten, Laura and van Iersel, Leo},
TITLE = {Nonbinary tree-based phylogenetic networks},
YEAR = {2018},
JOURNAL = {TCBB},
VOLUME = {15},
NUMBER = {1},
PAGES = {205-217},
URL = {http://dx.doi.org/10.1109/TCBB.2016.2615918},
NOTE = {http://arxiv.org/abs/1601.04974},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network}
}

3

Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, Vol. 15:398-410, 2018.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf.

@Article{HusonLinz2018,
AUTHOR = {Huson, Daniel H. and Linz, Simone},
TITLE = {Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees},
YEAR = {2018},
JOURNAL = {TCBB},
VOLUME = {15},
PAGES = {398-410},
URL = {http://dx.doi.org/10.1109/TCBB.2016.2537326},
NOTE = {https://simonelinz.files.wordpress.com/2016/06/hl16.pdf},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction}
}

4

Andrew R. Francis, Charles Semple and Mike Steel. New characterisations of tree-based networks and proximity measures. In Advances in Applied Mathematics, Vol. 93:93-107, 2018.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1611.04225.

@Article{FSS2018,
AUTHOR = {Francis, Andrew R. and Semple, Charles and Steel, Mike},
TITLE = {New characterisations of tree-based networks and proximity measures},
YEAR = {2018},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {93},
PAGES = {93-107},
URL = {http://doi.org/10.1016/j.aam.2017.08.003},
NOTE = {https://arxiv.org/abs/1611.04225},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network}
}

5

Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. In RECOMB-CG18, Vol. 11183:309-323 of LNCS, Springer, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.06364.

@InProceedings{Weller2018,
AUTHOR = {Weller, Mathias},
TITLE = {Linear-Time Tree Containment in Phylogenetic Networks},
YEAR = {2018},
BOOKTITLE = {RECOMB-CG18},
VOLUME = {11183},
PAGES = {309-323},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-00834-5_18},
NOTE = {https://arxiv.org/abs/1702.06364},
KEYWORDS = {explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment}
}

6

Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):1229-1248, 2018.
Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance.
Note: https://arxiv.org/abs/1702.05609.

@Article{FHMW2018,
AUTHOR = {Francis, Andrew R. and Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Bounds for phylogenetic network space metrics},
YEAR = {2018},
JOURNAL = {JOMB},
VOLUME = {76},
NUMBER = {5},
PAGES = {1229-1248},
URL = {https://dx.doi.org/10.1007/s00285-017-1171-0},
NOTE = {https://arxiv.org/abs/1702.05609},
KEYWORDS = {bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance}
}

7

Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data. In RECOMB-CG18, Vol. 11183:242-259 of LNCS, Springer, 2018.
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: http://biorxiv.org/content/early/2017/05/01/132795.

@InProceedings{HVBL2018,
AUTHOR = {Hejase, Hussein A. and VandePol, Natalie and Bonito, Gregory A. and Liu, Kevin J.},
TITLE = {Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data},
YEAR = {2018},
BOOKTITLE = {RECOMB-CG18},
VOLUME = {11183},
PAGES = {242-259},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-00834-5_14},
NOTE = {http://biorxiv.org/content/early/2017/05/01/132795},
KEYWORDS = {explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction}
}

8

Andrew R. Francis, Katharina Huber and Vincent Moulton. Tree-based unrooted phylogenetic networks. In BMB, Vol. 80(2):404-416, 2018.
Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network.
Note: https://arxiv.org/abs/1704.02062.

@Article{FHM2018,
AUTHOR = {Francis, Andrew R. and Huber, Katharina and Moulton, Vincent},
TITLE = {Tree-based unrooted phylogenetic networks},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
NUMBER = {2},
PAGES = {404-416},
URL = {https://doi.org/10.1007/s11538-017-0381-3},
NOTE = {https://arxiv.org/abs/1704.02062},
KEYWORDS = {characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network}
}

9

Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, Vol. 80(8):2240-2259, 2018.
Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.

@Article{BST2018,
AUTHOR = {Bordewich, Magnus and Semple, Charles and Tokac, Nihan},
TITLE = {Constructing tree-child networks from distance matrices},
YEAR = {2018},
JOURNAL = {Algorithmica},
VOLUME = {80},
NUMBER = {8},
PAGES = {2240-2259},
URL = {http://dx.doi.org/10.1007/s00453-017-0320-6},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf},
KEYWORDS = {compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness}
}

10

Andreas Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time. In AlCoB18, Vol. 10849:24-36 of LNCS, Springer, 2018.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.04088.

@InProceedings{Gunawan2018,
AUTHOR = {Gunawan, Andreas},
TITLE = {Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time},
YEAR = {2018},
BOOKTITLE = {AlCoB18},
VOLUME = {10849},
PAGES = {24-36},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-319-91938-6_3},
NOTE = {https://arxiv.org/abs/1702.04088},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}

11

Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:62-79, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/.

@Article{GGLVZ2018,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}�phane and Zhang, Louxin},
TITLE = {Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks},
YEAR = {2018},
JOURNAL = {DAM},
VOLUME = {246},
PAGES = {62-79},
URL = {http://dx.doi.org/10.1016/j.dam.2017.07.015},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/},
KEYWORDS = {explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

12

Remie Janssen, Mark Jones, Péter L. Erdös, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):2177-2208, 2018.
Keywords: distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1708.07656.

@Article{JJEIS2018,
AUTHOR = {Janssen, Remie and Jones, Mark and Erd{\~A}�s, P{\~A}�ter L. and van Iersel, Leo and Scornavacca, Celine},
TITLE = {Exploring the tiers of rooted phylogenetic network space using tail moves},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
NUMBER = {8},
PAGES = {2177-2208},
URL = {http://dx.doi.org/10.1007/s11538-018-0452-0},
NOTE = {https://arxiv.org/abs/1708.07656},
KEYWORDS = {distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance}
}

13

Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. In JGAA, Vol. 22(2):329-355, 2018.
Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree-child network.
Note: https://arxiv.org/abs/1707.09579

@Article{Klawitter2018b,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The SNPR neighbourhood of tree-child networks},
YEAR = {2018},
JOURNAL = {JGAA},
VOLUME = {22},
NUMBER = {2},
PAGES = {329-355},
URL = {http://dx.doi.org/10.7155/jgaa.00472},
NOTE = {https://arxiv.org/abs/1707.09579 KEYWORDS = {distance between networks, phylogenetic network, phylogeny, SPR distance, tree-child network}
}

14

Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):1057-1058, 2018.
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.

@Article{BMSWBM2018,
AUTHOR = {Bastkowski, Sarah and Mapleson, Daniel and Spillner, Andreas and Wu, Taoyang and Balvociute, Monika and Moulton, Vincent},
TITLE = {SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution},
YEAR = {2018},
JOURNAL = {BIO},
VOLUME = {34},
NUMBER = {6},
PAGES = {1057-1058},
URL = {https://doi.org/10.1093/bioinformatics/btx740},
NOTE = {https://doi.org/10.1101/169177},
KEYWORDS = {abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network}
}

15

Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167-176 of LNCS, Springer, 2018.
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/abs/1707.05722.

@InProceedings{RW2018,
AUTHOR = {Roch, Sebastien and Wang, Kun-Chieh},
TITLE = {Circular Networks from Distorted Metrics},
YEAR = {2018},
BOOKTITLE = {RECOMB18},
VOLUME = {10812},
PAGES = {167-176},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-319-89929-9_11},
NOTE = {https://arxiv.org/abs/1707.05722},
KEYWORDS = {abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network}
}

16

Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, Vol. 67(5):800-820, 2018.
Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050.

@Article{BSKSA2018,
AUTHOR = {Bastide, Paul and Sol{\~A}�s-Lemus, Claudia and Kriebel, Ricardo and Sparks, Kenneth William and An{\~A}�, C{\~A}�cile},
TITLE = {Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {5},
PAGES = {800-820},
URL = {http://dx.doi.org/10.1093/sysbio/syy033},
NOTE = {https://doi.org/10.1101/194050},
KEYWORDS = {ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test}
}

17

Katharina Huber, Vincent Moulton, Charles Semple and Taoyang Wu. Quarnet inference rules for level-1 networks. In BMB, Vol. 80:2137-2153, 2018.
Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: https://arxiv.org/abs/1711.06720.

@Article{HMSW2018,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Semple, Charles and Wu, Taoyang},
TITLE = {Quarnet inference rules for level-1 networks},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
PAGES = {2137-2153},
URL = {https://doi.org/10.1007/s11538-018-0450-2},
NOTE = {https://arxiv.org/abs/1711.06720},
KEYWORDS = {explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

18

Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks. In SIAM Journal on Discrete Mathematics, Vol. 32(3):2047-2066, 2018.
Keywords: explicit network, from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/1701.08982.

@Article{IerselMoulton2018,
AUTHOR = {van Iersel, Leo and Moulton, Vincent},
TITLE = {Leaf-reconstructibility of phylogenetic networks},
YEAR = {2018},
JOURNAL = {SIAM Journal on Discrete Mathematics},
VOLUME = {32},
NUMBER = {3},
PAGES = {2047-2066},
URL = {https://dx.doi.org/10.1137/17M1111930},
NOTE = {https://arxiv.org/abs/1701.08982},
KEYWORDS = {explicit network, from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

19

Kristina Wicke and Mareike Fischer. Phylogenetic diversity and biodiversity indices on phylogenetic networks. In MB, Vol. 298:80-90, 2018.
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1706.05279.

@Article{WickeFischer2018,
AUTHOR = {Wicke, Kristina and Fischer, Mareike},
TITLE = {Phylogenetic diversity and biodiversity indices on phylogenetic networks},
YEAR = {2018},
JOURNAL = {MB},
VOLUME = {298},
PAGES = {80-90},
URL = {https://doi.org/10.1016/j.mbs.2018.02.005},
NOTE = {https://arxiv.org/abs/1706.05279},
KEYWORDS = {diversity, explicit network, from network, normal network, phylogenetic network, phylogeny}
}

20

Magnus Bordewich and Charles Semple. A universal tree-based network with the minimum number of reticulations. In DAM, Vol. 250:357-362, 2018.
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: https://arxiv.org/abs/1707.08274.

@Article{BordewichSemple2018b,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {A universal tree-based network with the minimum number of reticulations},
YEAR = {2018},
JOURNAL = {DAM},
VOLUME = {250},
PAGES = {357-362},
URL = {https://doi.org/10.1016/j.dam.2018.05.010},
NOTE = {https://arxiv.org/abs/1707.08274},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, tree-based network}
}

21

Janosch Döcker and Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.04127.

@Article{DöckerLinz2018,
AUTHOR = {D{\~A}�cker, Janosch and Linz, Simone},
TITLE = {On the existence of a cherry-picking sequence},
YEAR = {2018},
JOURNAL = {TCS},
VOLUME = {714},
PAGES = {36-50},
URL = {https://doi.org/10.1016/j.tcs.2017.12.005},
NOTE = {https://arxiv.org/abs/1712.04127},
KEYWORDS = {cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network}
}

22

Elizabeth Gross and Colby Long. Distinguishing Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 2(1):72-93, 2018.
Keywords: distinguishability, phylogenetic network, phylogeny, semidirected network, statistical model, uniqueness.
Note: https://arxiv.org/abs/1706.03060.

@Article{GrossLong2018,
AUTHOR = {Gross, Elizabeth and Long, Colby},
TITLE = {Distinguishing Phylogenetic Networks},
YEAR = {2018},
JOURNAL = {SIAM Journal on Applied Algebra and Geometry},
VOLUME = {2},
NUMBER = {1},
PAGES = {72-93},
URL = {https://doi.org/10.1137/17M1134238},
NOTE = {https://arxiv.org/abs/1706.03060},
KEYWORDS = {distinguishability, phylogenetic network, phylogeny, semidirected network, statistical model, uniqueness}
}

23

James H. Degnan. Modeling Hybridization Under the Network Multispecies Coalescent. In SB, Vol. 67(5):786-799, 2018.
Keywords: distance between networks, phylogenetic network, phylogeny, reconstruction, survey.
Note: https://academic.oup.com/sysbio/article/67/5/786/5017269.

@Article{Degnan2018,
AUTHOR = {Degnan, James H.},
TITLE = {Modeling Hybridization Under the Network Multispecies Coalescent},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {5},
PAGES = {786-799},
URL = {https://doi.org/10.1093/sysbio/syy040},
NOTE = {https://academic.oup.com/sysbio/article/67/5/786/5017269},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, reconstruction, survey}
}

24

Andrew R. Francis and Vincent Moulton. Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. In JTB, Vol. 446:160-167, 2018.
Keywords: explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness.
Note: https://arxiv.org/abs/1712.04223.

@Article{FrancisMoulton2018,
AUTHOR = {Francis, Andrew R. and Moulton, Vincent},
TITLE = {Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution},
YEAR = {2018},
JOURNAL = {JTB},
VOLUME = {446},
PAGES = {160-167},
URL = {https://doi.org/10.1016/j.jtbi.2018.03.011},
NOTE = {https://arxiv.org/abs/1712.04223},
KEYWORDS = {explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness}
}

25

Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.

@Article{IJS2018,
AUTHOR = {van Iersel, Leo and Jones, Mark and Scornavacca, Celine},
TITLE = {Improved maximum parsimony models for phylogenetic networks},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {3},
PAGES = {518-542},
URL = {https://dx.doi.org/10.1093/sysbio/syx094},
NOTE = {https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf},
KEYWORDS = {explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying}
}

26

Sajad Mirzaei. Efficient Algorithms for Trees and Networks in Evolutionary Genomics. PhD thesis, University of Connecticut, 2018.
Keywords: branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction.
Note: https://opencommons.uconn.edu/dissertations/1853.

@PhdThesis{Sajad2018,
AUTHOR = {Mirzaei, Sajad},
TITLE = {Efficient Algorithms for Trees and Networks in Evolutionary Genomics},
YEAR = {2018},
SCHOOL = {University of Connecticut},
URL = {https://opencommons.uconn.edu/dissertations/1853},
NOTE = {https://opencommons.uconn.edu/dissertations/1853},
KEYWORDS = {branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction}
}

27

Charles Semple and Jack Simpson. When is a phylogenetic network simply an amalgamation of two trees? In BMB, Vol. 80(9):2338-2348, 2018.
Keywords: characterization, phylogenetic network, phylogeny, reticulation-visible network, stack-free network, tree-based network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS18.pdf.

@Article{SempleSimpson2018,
AUTHOR = {Semple, Charles and Simpson, Jack},
TITLE = {When is a phylogenetic network simply an amalgamation of two trees?},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
NUMBER = {9},
PAGES = {2338-2348},
URL = {https://doi.org/10.1007/s11538-018-0463-x},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/SS18.pdf},
KEYWORDS = {characterization, phylogenetic network, phylogeny, reticulation-visible network, stack-free network, tree-based network}
}

28

Magnus Bordewich, Katharina Huber, Vincent Moulton and Charles Semple. Recovering normal networks from shortest inter-taxa distance information. In JOMB, Vol. 77(3):571-594, 2018.
Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.

@Article{BHMS2018,
AUTHOR = {Bordewich, Magnus and Huber, Katharina and Moulton, Vincent and Semple, Charles},
TITLE = {Recovering normal networks from shortest inter-taxa distance information},
YEAR = {2018},
JOURNAL = {JOMB},
VOLUME = {77},
NUMBER = {3},
PAGES = {571-594},
URL = {http://dx.doi.org/10.1007/s00285-018-1218-x},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf},
KEYWORDS = {explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness}
}

29

Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: https://dx.doi.org/10.1093/molbev/msx307.

@Article{ZODT2018,
AUTHOR = {Zhang, Chi and Ogilvie, Huw A. and Drummond, Alexei J. and Stadler, Tanja},
TITLE = {Bayesian Inference of Species Networks from Multilocus Sequence Data},
YEAR = {2018},
JOURNAL = {MBE},
VOLUME = {35},
NUMBER = {2},
PAGES = {504-517},
URL = {https://dx.doi.org/10.1093/molbev/msx307},
NOTE = {https://dx.doi.org/10.1093/molbev/msx307},
KEYWORDS = {bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model}
}

30

Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018.
Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.

@PhdThesis{Scholz2018,
AUTHOR = {Scholz, Guillaume},
TITLE = {New algorithms and mathematical tools for phylogenetics beyond trees},
YEAR = {2018},
SCHOOL = {University of East Anglia},
NOTE = { https://ueaeprints.uea.ac.uk/id/eprint/66952},
KEYWORDS = {circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness}
}

31

Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In JCB, Vol. 25(3):253-269, 2018.
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.

@Article{CCYH2018,
AUTHOR = {Chang, Kuang-Yu and Cui, Yun and Yiu, Siu-Ming and Hon, Wing-Kai},
TITLE = {Reconstructing One-Articulated Networks with Distance Matrices},
YEAR = {2018},
JOURNAL = {JCB},
VOLUME = {25},
NUMBER = {3},
PAGES = {253-269},
URL = {http://dx.doi.org/10.1089/cmb.2017.0148},
KEYWORDS = {explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction}
}

32

Kuang-Yu Chang, Wing-Kai Hon and Sharma V. Thankachan. Compact Encoding for Galled-Trees and its Applications. In 2018 Data Compression Conference, Pages 297-306, 2018.
Keywords: compression, counting, explicit network, galled tree, phylogenetic network, polynomial.

@InProceedings{CHT2018,
AUTHOR = {Chang, Kuang-Yu and Hon, Wing-Kai and Thankachan, Sharma V.},
TITLE = {Compact Encoding for Galled-Trees and its Applications},
YEAR = {2018},
BOOKTITLE = {2018 Data Compression Conference},
PAGES = {297-306},
URL = {http://dx.doi.org/10.1109/DCC.2018.00038},
KEYWORDS = {compression, counting, explicit network, galled tree, phylogenetic network, polynomial}
}

33

Hongwei Yan, Andreas Gunawan and Louxin Zhang. S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. In BIO, Vol. 34(17):i680–i686, 2018.
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, SAT.
Note: http://dx.doi.org/10.1093/bioinformatics/bty594.

@Article{YGZ2018,
AUTHOR = {Yan, Hongwei and Gunawan, Andreas and Zhang, Louxin},
TITLE = {S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks},
YEAR = {2018},
JOURNAL = {BIO},
VOLUME = {34},
NUMBER = {17},
PAGES = {i680{\^a}��i686},
URL = {http://dx.doi.org/10.1093/bioinformatics/bty594},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/bty594},
KEYWORDS = {cluster containment, explicit network, phylogenetic network, phylogeny, SAT}
}

34

Michael Hendriksen. Tree-based unrooted nonbinary phylogenetic networks. In MBIO, Vol. 302:131-138, 2018.
Keywords: characterization, phylogenetic network, phylogeny, tree-based network, unrooted tree-based network.

@Article{Hendriksen2018,
AUTHOR = {Hendriksen, Michael},
TITLE = {Tree-based unrooted nonbinary phylogenetic networks},
YEAR = {2018},
JOURNAL = {MBIO},
VOLUME = {302},
PAGES = {131-138},
URL = {http://dx.doi.org/10.1016/j.mbs.2018.06.005},
KEYWORDS = {characterization, phylogenetic network, phylogeny, tree-based network, unrooted tree-based network}
}

35

Dingqiao Wen, Yun Yu, Jiafan Zhu and Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735-740, 2018.
Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.

@Article{WYZN2018,
AUTHOR = {Wen, Dingqiao and Yu, Yun and Zhu, Jiafan and Nakhleh, Luay},
TITLE = {Inferring Phylogenetic Networks Using PhyloNet},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {4},
PAGES = {735-740},
URL = {http://dx.doi.org/10.1093/sysbio/syy015},
KEYWORDS = {bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software}
}

36

Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt and Luay Nakhleh. Bayesian inference of phylogenetic networks from bi-allelic genetic markers. In PLoS Computational Biology, Vol. 14(1):e1005932.1-32, 2018.
Keywords: bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet.
Note: https://doi.org/10.1371/journal.pcbi.1005932.

@Article{ZWYMN2018,
AUTHOR = {Zhu, Jiafan and Wen, Dingqiao and Yu, Yun and Meudt, Heidi M. and Nakhleh, Luay},
TITLE = {Bayesian inference of phylogenetic networks from bi-allelic genetic markers},
YEAR = {2018},
JOURNAL = {PLoS Computational Biology},
VOLUME = {14},
NUMBER = {1},
PAGES = {e1005932.1-32},
URL = {https://doi.org/10.1371/journal.pcbi.1005932},
NOTE = {https://doi.org/10.1371/journal.pcbi.1005932},
KEYWORDS = {bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet}
}

37

Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.

@Article{WenNakhleh2018,
AUTHOR = {Wen, Dingqiao and Nakhleh, Luay},
TITLE = {Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {3},
PAGES = {439-457},
URL = {https://doi.org/10.1093/sysbio/syx085},
NOTE = {https://doi.org/10.1093/sysbio/syx085},
KEYWORDS = {bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}

38

Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018.
Keywords: cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment.
Note: https://scholarbank.nus.edu.sg/handle/10635/144270.

@PhdThesis{Gunawan2018b,
AUTHOR = {Gunawan, Andreas},
TITLE = {On the tree and cluster containment problems for phylogenetic networks},
YEAR = {2018},
SCHOOL = {National University of Singapore},
URL = {https://scholarbank.nus.edu.sg/handle/10635/144270},
NOTE = {https://scholarbank.nus.edu.sg/handle/10635/144270},
KEYWORDS = {cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment}
}

39

Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems. In AlCoB18, Vol. 10849:37-49 of LNCS, Springer, 2018.
Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, polynomial, reconstruction, weakly displaying.
Note: https://research.tudelft.nl/files/53686721/10.1007_978_3_319_91938_6_4.pdf.

@InProceedings{IJJYZ2018,
AUTHOR = {van Iersel, Leo and Janssen, Remie and Jones, Mark and Murakami, Yukihiro and Zeh, Norbert},
TITLE = {Polynomial-Time Algorithms for Phylogenetic Inference Problems},
YEAR = {2018},
BOOKTITLE = {AlCoB18},
VOLUME = {10849},
PAGES = {37-49},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-319-91938-6_4},
NOTE = {https://research.tudelft.nl/files/53686721/10.1007_978_3_319_91938_6_4.pdf},
KEYWORDS = {hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, polynomial, reconstruction, weakly displaying}
}

2017

1

Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.
Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.

@Article{HIMSW2017,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Moulton, Vincent and Scornavacca, Celine and Wu, Taoyang},
TITLE = {Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets},
YEAR = {2017},
JOURNAL = {ALG},
VOLUME = {77},
NUMBER = {1},
PAGES = {173-200},
URL = {http://dx.doi.org/10.1007/s00453-015-0069-8},
NOTE = {http://arxiv.org/abs/1411.6804},
KEYWORDS = {explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction}
}

2

Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.

@Article{BFLS2017,
AUTHOR = {Bryant, Christopher and Fischer, Mareike and Linz, Simone and Semple, Charles},
TITLE = {On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {417},
PAGES = {100-108},
URL = {http://dx.doi.org/10.1016/j.jtbi.2017.01.013},
NOTE = {http://arxiv.org/abs/1505.06898},
KEYWORDS = {explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny}
}

3

Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017.
Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network.
Note: http://arxiv.org/abs/1509.06104v1.

@Article{BBS2017,
AUTHOR = {Balvociute, Monika and Bryant, David and Spillner, Andreas},
TITLE = {When can splits be drawn in the plane?},
YEAR = {2017},
JOURNAL = {SIAM Journal on Discrete Mathematics},
VOLUME = {31},
NUMBER = {2},
PAGES = {839-856},
URL = {http://dx.doi.org/10.1137/15M1040852},
NOTE = {http://arxiv.org/abs/1509.06104v1},
KEYWORDS = {abstract network, characterization, flat, phylogenetic network, planar, split, split network}
}

4

Satyan L. Devadoss and Samantha Petti. A Space of Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 1(1):683-705, 2017.
Keywords: abstract network, circular split system, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/1607.06978.

@Article{DevadossPetti2017,
AUTHOR = {Devadoss, Satyan L. and Petti, Samantha},
TITLE = {A Space of Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {SIAM Journal on Applied Algebra and Geometry},
VOLUME = {1},
NUMBER = {1},
PAGES = {683-705},
URL = {https://dx.doi.org/10.1137/16M1103129},
NOTE = {http://arxiv.org/abs/1607.06978},
KEYWORDS = {abstract network, circular split system, phylogenetic network, phylogeny, split network}
}

5

Charles Semple. Size of a phylogenetic network. In DAM, Vol. 217(2):362-367, 2017.
Keywords: compressed network, number of vertices, phylogenetic network, phylogeny, stack-free network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf.

@Article{Semple2017,
AUTHOR = {Semple, Charles},
TITLE = {Size of a phylogenetic network},
YEAR = {2017},
JOURNAL = {DAM},
VOLUME = {217},
NUMBER = {2},
PAGES = {362-367},
URL = {http://dx.doi.org/10.1016/j.dam.2016.09.004},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf},
KEYWORDS = {compressed network, number of vertices, phylogenetic network, phylogeny, stack-free network}
}

6

Philippe Gambette, Katharina Huber and Steven Kelk. On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. In JOMB, Vol. 74(7):1729-1751, 2017.
Keywords: from clusters, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1007/s00285-016-1068-3.

@Article{GHK2017,
AUTHOR = {Gambette, Philippe and Huber, Katharina and Kelk, Steven},
TITLE = {On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters},
YEAR = {2017},
JOURNAL = {JOMB},
VOLUME = {74},
NUMBER = {7},
PAGES = {1729-1751},
URL = {http://dx.doi.org/10.1007/s00285-016-1068-3},
NOTE = {http://dx.doi.org/10.1007/s00285-016-1068-3},
KEYWORDS = {from clusters, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

7

Philippe Gambette, Katharina Huber and Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 2017.
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.

@Article{GHS2017,
AUTHOR = {Gambette, Philippe and Huber, Katharina and Scholz, Guillaume},
TITLE = {Uprooted Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {BMB},
VOLUME = {79},
NUMBER = {9},
PAGES = {2022-2048},
URL = {http://dx.doi.org/10.1007/s11538-017-0318-x},
NOTE = {http://arxiv.org/abs/1511.08387},
KEYWORDS = {circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness}
}

8

Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.

@Article{MKSWG2017,
AUTHOR = {Matsieva, Julia and Kelk, Steven and Scornavacca, Celine and Whidden, Chris and Gusfield, Dan},
TITLE = {A Resolution of the Static Formulation Question for the Problem of Computing the History Bound},
YEAR = {2017},
JOURNAL = {TCBB},
VOLUME = {14},
NUMBER = {2},
PAGES = {404-417},
URL = {http://dx.doi.org/10.1109/TCBB.2016.2527645},
KEYWORDS = {ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny}
}

9

Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.

@Article{ShaDegnan2017,
AUTHOR = {Zhu, Sha and Degnan, James H.},
TITLE = {Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent},
YEAR = {2017},
JOURNAL = {SB},
VOLUME = {66},
NUMBER = {2},
PAGES = {283-298},
URL = {http://dx.doi.org/10.1093/sysbio/syw097},
NOTE = {presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g},
KEYWORDS = {branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness}
}

10

Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017.
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.

@Article{KordiBansal2017,
AUTHOR = {Kordi, Misagh and Bansal, Mukul S.},
TITLE = {On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees},
YEAR = {2017},
JOURNAL = {TCBB},
VOLUME = {14},
NUMBER = {3},
PAGES = {587-599},
URL = {http://dx.doi.org/10.1109/TCBB.2015.2511761},
NOTE = {http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf},
KEYWORDS = {duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction}
}

11

Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.

@Article{GDZ2017,
AUTHOR = {Gunawan, Andreas and DasGupta, Bhaskar and Zhang, Louxin},
TITLE = {A decomposition theorem and two algorithms for reticulation-visible networks},
YEAR = {2017},
JOURNAL = {Information and Computation},
VOLUME = {252},
PAGES = {161-175},
URL = {http://dx.doi.org/10.1016/j.ic.2016.11.001},
NOTE = {https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf},
KEYWORDS = {cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}

12

Gabriel Cardona and Joan Carles Pons. Reconstruction of LGT networks from tri-LGT-nets. In JOMB, Vol. 75(6-7):1669-1692, 2017.
Keywords: explicit network, from subnetworks, from tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1007/s00285-017-1171-0.

@Article{CardonaPons2017,
AUTHOR = {Cardona, Gabriel and Pons, Joan Carles},
TITLE = {Reconstruction of LGT networks from tri-LGT-nets},
YEAR = {2017},
JOURNAL = {JOMB},
VOLUME = {75},
NUMBER = {6-7},
PAGES = {1669-1692},
URL = {http://dx.doi.org/10.1007/s00285-017-1131-8},
NOTE = {https://doi.org/10.1007/s00285-017-1171-0},
KEYWORDS = {explicit network, from subnetworks, from tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

13

Bingxin Lu, Louxin Zhang and Hon Wai Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017.
Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork.
Note: http://dx.doi.org/10.1186/s12864-017-3500-5.

@InProceedings{LZL2017,
AUTHOR = {Lu, Bingxin and Zhang, Louxin and Leong, Hon Wai},
TITLE = {A program to compute the soft Robinson-Foulds distance between phylogenetic networks},
YEAR = {2017},
BOOKTITLE = {APBC17},
VOLUME = {18},
NUMBER = {Suppl. 2},
PAGES = {111},
SERIES = {BMC Genomics},
URL = {http://dx.doi.org/10.1186/s12864-017-3500-5},
NOTE = {http://dx.doi.org/10.1186/s12864-017-3500-5},
KEYWORDS = {cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork}
}

14

Vincent Moulton, James Oldman and Taoyang Wu. A cubic-time algorithm for computing the trinet distance between level-1 networks. In IPL, Vol. 123:36-41, 2017.
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet.
Note: https://doi.org/10.1016/j.ipl.2017.03.002.

@Article{MOW2017,
AUTHOR = {Moulton, Vincent and Oldman, James and Wu, Taoyang},
TITLE = {A cubic-time algorithm for computing the trinet distance between level-1 networks},
YEAR = {2017},
JOURNAL = {IPL},
VOLUME = {123},
PAGES = {36-41},
URL = {https://doi.org/10.1016/j.ipl.2017.03.002},
NOTE = {https://doi.org/10.1016/j.ipl.2017.03.002},
KEYWORDS = {distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet}
}

15

Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.

@Article{KamnevaRosenberg2017,
AUTHOR = {Kamneva, Olga K. and Rosenberg, Noah A.},
TITLE = {Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting},
YEAR = {2017},
JOURNAL = {Evolutionary Bioinformatics},
VOLUME = {13},
NUMBER = {1176934317691935},
PAGES = {1-16},
URL = {https://dx.doi.org/10.1177%2F1176934317691935},
NOTE = {https://dx.doi.org/10.1177%2F1176934317691935},
KEYWORDS = {evaluation, explicit network, incomplete lineage sorting, simulation}
}

16

Magnus Bordewich, Simone Linz and Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.

@Article{BLS2017,
AUTHOR = {Bordewich, Magnus and Linz, Simone and Semple, Charles},
TITLE = {Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {423},
PAGES = {1-12},
URL = {https://doi.org/10.1016/j.jtbi.2017.03.032},
NOTE = {https://simonelinz.files.wordpress.com/2017/04/bls171.pdf},
KEYWORDS = {distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network}
}

17

Celine Scornavacca, Joan Carles Pons and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.

@Article{SPC2017,
AUTHOR = {Scornavacca, Celine and Pons, Joan Carles and Cardona, Gabriel},
TITLE = {Fast algorithm for the reconciliation of gene trees and LGT networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {418},
PAGES = {129-137},
URL = {https://doi.org/10.1016/j.jtbi.2017.01.024},
KEYWORDS = {duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}

18

Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .

@InProceedings{JRS2017,
AUTHOR = {Jansson, Jesper and Rajaby, Ramesh and Sung, Wing-Kin},
TITLE = {An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees},
YEAR = {2017},
BOOKTITLE = {AlCoB17},
VOLUME = {10252},
PAGES = {115-126},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-58163-7_8},
NOTE = {},
KEYWORDS = {distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance}
}

19

Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.

@Article{IMSW2017,
AUTHOR = {van Iersel, Leo and Moulton, Vincent and De Swart, Eveline and Wu, Taoyang},
TITLE = {Binets: fundamental building blocks for phylogenetic networks},
YEAR = {2017},
JOURNAL = {BMB},
VOLUME = {79},
NUMBER = {5},
PAGES = {1135-1154},
URL = {http://dx.doi.org/10.1007/s11538-017-0275-4},
NOTE = {http://dx.doi.org/10.1007/s11538-017-0275-4},
KEYWORDS = {approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction}
}

20

Juan Wang and Maozu Guo. A Metric on the Space of kth-order reduced Phylogenetic Networks. In Scientific Reports, Vol. 7(3189):1-10, 2017.
Keywords: distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial.
Note: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/.

@Article{WangGuo2017,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {A Metric on the Space of kth-order reduced Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {Scientific Reports},
VOLUME = {7},
NUMBER = {3189},
PAGES = {1-10},
URL = {https://dx.doi.org/10.1038/s41598-017-03363-y},
NOTE = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/},
KEYWORDS = {distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial}
}

21

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.1-21, 2017.
Keywords: distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.

@Article{GIJLPS2017,
AUTHOR = {Gambette, Philippe and van Iersel, Leo and Jones, Mark and Lafond, Manuel and Pardi, Fabio and Scornavacca, Celine},
TITLE = {Rearrangement Moves on Rooted Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {PLoS Computational Biology},
VOLUME = {13},
NUMBER = {8},
PAGES = {e1005611.1-21},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1005611},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/},
KEYWORDS = {distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance}
}

22

Han Lai, Maureen Stolzer and Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMB-CG17, Vol. 10562:298-320 of LNCS, Springer, 2017.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.

@InProceedings{LSD2017,
AUTHOR = {Lai, Han and Stolzer, Maureen and Durand, Dannie},
TITLE = {Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses},
YEAR = {2017},
BOOKTITLE = {RECOMB-CG17},
VOLUME = {10562},
PAGES = {298-320},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-67979-2_16},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction}
}

23

Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.

@Article{CBA2017,
AUTHOR = {Sol{\~A}�s-Lemus, Claudia and Bastide, Paul and An{\~A}�, C{\~A}�cile},
TITLE = {PhyloNetworks: A Package for Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {MBE},
VOLUME = {34},
NUMBER = {12},
PAGES = {3292-3298},
URL = {http://dx.doi.org/10.1093/molbev/msx235},
NOTE = {https://doi.org/10.1093/molbev/msx235},
KEYWORDS = {from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software}
}

24

Ruzbeh Tusserkani, Hadi Poormohammadi, Azin Azadi and Changiz Eslahchi. Inferring phylogenies from minimal information. In AEEICB17, Pages 202-206, IEEE, 2017.
Keywords: from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction.

@InProceedings{TPAE2017,
AUTHOR = {Tusserkani, Ruzbeh and Poormohammadi, Hadi and Azadi, Azin and Eslahchi, Changiz},
TITLE = {Inferring phylogenies from minimal information},
YEAR = {2017},
BOOKTITLE = {AEEICB17},
PAGES = {202-206},
PUBLISHER = {IEEE},
URL = {https://doi.org/10.1109/AEEICB.2017.7972412},
KEYWORDS = {from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction}
}

25

Klaus Schliep, Alastair J. Potts, David A. Morrison and Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017.
Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization.
Note: http://dx.doi.org/10.1111/2041-210X.12760.

@Article{KPMG2017,
AUTHOR = {Schliep, Klaus and Potts, Alastair J. and Morrison, David A. and Grimm, Guido W.},
TITLE = {Intertwining phylogenetic trees and networks},
YEAR = {2017},
JOURNAL = {Methods in Ecology and Evolution},
VOLUME = {8},
NUMBER = {10},
PAGES = {1212-1220},
NOTE = {http://dx.doi.org/10.1111/2041-210X.12760},
KEYWORDS = {abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization}
}

26

Timothy G. Vaughan. IcyTree: rapid browser-based visualization for phylogenetic trees and networks. In BIO, Vol. 33(15):2392-2394, 2017.
Keywords: ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btx155.

@Article{Vaughan2017,
AUTHOR = {Vaughan, Timothy G.},
TITLE = {IcyTree: rapid browser-based visualization for phylogenetic trees and networks},
YEAR = {2017},
JOURNAL = {BIO},
VOLUME = {33},
NUMBER = {15},
PAGES = {2392-2394},
URL = {http://dx.doi.org/10.1093/bioinformatics/btx155},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btx155},
KEYWORDS = {ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization}
}

27

Mohammad Hossein Reyhani and Hadi Poormohammadi. RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function. In Archives of Advances in Biosciences, Vol. 8(4):14-20, 2017.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://journals.sbmu.ac.ir/jps/article/view/16707.

@Article{ReyhaniPoormohammadi2017,
AUTHOR = {Reyhani, Mohammad Hossein and Poormohammadi, Hadi},
TITLE = {RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function},
YEAR = {2017},
JOURNAL = {Archives of Advances in Biosciences},
VOLUME = {8},
NUMBER = {4},
PAGES = {14-20},
URL = {https://doi.org/10.22037/jps.v8i4.16707},
NOTE = {http://journals.sbmu.ac.ir/jps/article/view/16707},
KEYWORDS = {explicit network, from triplets, heuristic, phylogenetic network, phylogeny, reconstruction}
}

28

Hussein A. Hejase. Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories. PhD thesis, Michigan State University, 2017.
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: https://dx.doi.org/10.25335/M5T855.

@PhdThesis{Hejase2017,
AUTHOR = {Hejase, Hussein A.},
TITLE = {Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories},
YEAR = {2017},
SCHOOL = {Michigan State University},
URL = {http://dx.doi.org/10.25335/M5T855},
NOTE = {https://dx.doi.org/10.25335/M5T855},
KEYWORDS = {explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction}
}

29

Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.

@Article{JWTS2017,
AUTHOR = {Jacox, Edwin and Weller, Mathias and Tannier, Eric and Scornavacca, Celine},
TITLE = {Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses},
YEAR = {2017},
JOURNAL = {BIO},
VOLUME = {33},
NUMBER = {7},
PAGES = {980-987},
URL = {http://dx.doi.org/10.1093/bioinformatics/btw778},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btw778},
KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

30

Luay Nakhleh. Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees. Phyloseminar #70, 2017.
Keywords: bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model.
Note: https://www.youtube.com/watch?v=dkQsvLUUDcQ.

@Misc{Nakhleh2017,
AUTHOR = {Nakhleh, Luay},
TITLE = {Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees},
YEAR = {2017},
HOWPUBLISHED = {Phyloseminar #70},
NOTE = {https://www.youtube.com/watch?v=dkQsvLUUDcQ},
KEYWORDS = {bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model}
}

31

Celine Scornavacca. Occam's razor in phylogenetic network reconstruction. Phyloseminar #71, 2017.
Keywords: explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://www.youtube.com/watch?v=W6tEVulgQu8.

@Misc{Scornavacca2017,
AUTHOR = {Scornavacca, Celine},
TITLE = {Occam's razor in phylogenetic network reconstruction},
YEAR = {2017},
HOWPUBLISHED = {Phyloseminar #71},
NOTE = {https://www.youtube.com/watch?v=W6tEVulgQu8},
KEYWORDS = {explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction}
}

32

Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.

@Misc{Ane2017,
AUTHOR = {An{\~A}�, C{\~A}�cile},
TITLE = {From reconstructing to using phylogenetic networks},
YEAR = {2017},
HOWPUBLISHED = {Phyloseminar #72},
NOTE = {https://www.youtube.com/watch?v=PF4j_JOQP0c},
KEYWORDS = {explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network}
}

33

Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017.
Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model.
Note: https://tel.archives-ouvertes.fr/tel-01629648/en/, slides..

@PhdThesis{Bastide2017,
AUTHOR = {Bastide, Paul},
TITLE = {Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies},
YEAR = {2017},
SCHOOL = {Universit{\~A}� Paris Saclay},
NOTE = {https://tel.archives-ouvertes.fr/tel-01629648/en/, slides.},
KEYWORDS = {ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model}
}

34

Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:34-45 of LNCS, Springer, 2017.
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
Note: https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100.

@InProceedings{KYSW17,
AUTHOR = {Chang, Kuang-Yu and Cui, Yun and Yiu, Siu-Ming and Hon, Wing-Kai},
TITLE = {Reconstructing One-Articulated Networks with Distance Matrices},
YEAR = {2017},
BOOKTITLE = {ISBRA17},
VOLUME = {10330},
PAGES = {34-45},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://dx.doi.org/10.1007/978-3-319-59575-7_4},
NOTE = {https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100},
KEYWORDS = {explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction}
}

35

Dingqiao Wen. Bayesian Inference of Phylogenetic Networks from Sequence Data. PhD thesis, Rice University, 2017.
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, reconstruction.

@PhdThesis{Wen2017,
AUTHOR = {Wen, Dingqiao},
TITLE = {Bayesian Inference of Phylogenetic Networks from Sequence Data},
YEAR = {2017},
SCHOOL = {Rice University},
KEYWORDS = {bayesian, explicit network, phylogenetic network, phylogeny, reconstruction}
}

2016

1

Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1402.2136.

@Article{IKLWZ2016,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Whidden, Chris and Zeh, Norbert},
TITLE = {Hybridization Number on Three Rooted Binary Trees is EPT},
YEAR = {2016},
JOURNAL = {SIDMA},
VOLUME = {30},
NUMBER = {3},
PAGES = {1607-1631},
URL = {http://dx.doi.org/10.1137/15M1036579},
NOTE = {http://arxiv.org/abs/1402.2136},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction}
}

2

Katharina Huber, Vincent Moulton, Mike Steel and Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):1761-1780, 2016.
Keywords: compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1506.04438.

@Article{HMSW2016,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Steel, Mike and Wu, Taoyang},
TITLE = {Folding and unfolding phylogenetic trees and networks},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {73},
NUMBER = {6},
PAGES = {1761-1780},
URL = {http://dx.doi.org/10.1007/s00285-016-0993-5},
NOTE = {http://arxiv.org/abs/1506.04438},
KEYWORDS = {compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network}
}

3

Katharina Huber, Simone Linz, Vincent Moulton and Taoyang Wu. Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. In JOMB, Vol. 72(2):699-725, 2016.
Keywords: bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny.

@Article{HLMW2016,
AUTHOR = {Huber, Katharina and Linz, Simone and Moulton, Vincent and Wu, Taoyang},
TITLE = {Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {72},
NUMBER = {2},
PAGES = {699-725},
URL = {http://dx.doi.org/10.1007/s00285-015-0899-7},
KEYWORDS = {bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny}
}

4

Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189-215, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction.
Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.

@Article{KISW2016,
AUTHOR = {Kelk, Steven and van Iersel, Leo and Scornavacca, Celine and Weller, Mathias},
TITLE = {Phylogenetic incongruence through the lens of Monadic Second Order logic},
YEAR = {2016},
JOURNAL = {JGAA},
VOLUME = {20},
NUMBER = {2},
PAGES = {189-215},
URL = {http://dx.doi.org/10.7155/jgaa.00390},
NOTE = {http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction}
}

5

Stephen J. Willson. Comparing and simplifying distinct-cluster phylogenetic networks. In ACOM, Vol. 20(4):917-938, 2016.
Keywords: distinct-cluster network, explicit network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1501.07528.

@Article{Willson2016,
AUTHOR = {Willson, Stephen J.},
TITLE = {Comparing and simplifying distinct-cluster phylogenetic networks},
YEAR = {2016},
JOURNAL = {ACOM},
VOLUME = {20},
NUMBER = {4},
PAGES = {917-938},
URL = {http://dx.doi.org/10.1007/s00026-016-0324-y},
NOTE = {http://arxiv.org/abs/1501.07528},
KEYWORDS = {distinct-cluster network, explicit network, phylogenetic network, phylogeny}
}

6

Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. In RECOMB16, Vol. 9649:266 of LNBI, Springer, 2016.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: http://arxiv.org/abs/1507.02119.

@InProceedings{GDZ2016,
AUTHOR = {Gunawan, Andreas and DasGupta, Bhaskar and Zhang, Louxin},
TITLE = {Locating a Tree in a Reticulation-Visible Network in Cubic Time},
YEAR = {2016},
BOOKTITLE = {RECOMB16},
VOLUME = {9649},
PAGES = {266},
SERIES = {LNBI},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-31957-5},
NOTE = {http://arxiv.org/abs/1507.02119},
KEYWORDS = {cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}

7

Sajad Mirzaei and Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016.
Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software.
Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.

@Article{MirzaeiWu2016,
AUTHOR = {Mirzaei, Sajad and Wu, Yufeng},
TITLE = {Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees},
YEAR = {2016},
JOURNAL = {TCBB},
VOLUME = {13},
NUMBER = {3},
PAGES = {565-570},
URL = {http://dx.doi.org/10.1109/TCBB.2015.2462336},
NOTE = {http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf},
KEYWORDS = {bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software}
}

8

Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016.
Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .

@InProceedings{GGLVZ2016,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}�phane and Zhang, Louxin},
TITLE = {Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time},
YEAR = {2016},
BOOKTITLE = {IWOCA15},
VOLUME = {9538},
PAGES = {197-208},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-29516-9_17},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 },
KEYWORDS = {explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

9

Magnus Bordewich and Charles Semple. Reticulation-visible networks. In Advances in Applied Mathematics, Vol. 78:114-141, 2016.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf.

@Article{BordewichSemple2016b,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Reticulation-visible networks},
YEAR = {2016},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {78},
PAGES = {114-141},
URL = {http://dx.doi.org/10.1016/j.aam.2016.04.004},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment}
}

10

Louxin Zhang. On Tree-Based Phylogenetic Networks. In JCB, Vol. 23(7):553-565, 2016.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1509.01663.

@Article{Zhang2016,
AUTHOR = {Zhang, Louxin},
TITLE = {On Tree-Based Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {JCB},
VOLUME = {23},
NUMBER = {7},
PAGES = {553-565},
URL = {http://dx.doi.org/10.1089/cmb.2015.0228},
NOTE = {http://arxiv.org/abs/1509.01663},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network}
}

11

Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.

@Article{RSDB2016,
AUTHOR = {Ranwez, Vincent and Scornavacca, Celine and Doyon, Jean-Philippe and Berry, Vincent},
TITLE = {Inferring gene duplications, transfers and losses can be done in a discrete framework},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {72},
NUMBER = {7},
PAGES = {1811-1844},
URL = {http://dx.doi.org/10.1007/s00285-015-0930-z},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

12

Claudia Solís-Lemus and Cécile Ané. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. In PLOS Genetics, Vol. 12(3):e1005896, 2016.
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ.
Note: http://arxiv.org/abs/1509.06075v1.

@Article{SolisLemusAne2016,
AUTHOR = {Sol{\~A}�s-Lemus, Claudia and An{\~A}�, C{\~A}�cile},
TITLE = {Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting},
YEAR = {2016},
JOURNAL = {PLOS Genetics},
VOLUME = {12},
NUMBER = {3},
PAGES = {e1005896},
URL = {http://dx.doi.org/10.1371/journal.pgen.1005896},
NOTE = {http://arxiv.org/abs/1509.06075v1},
KEYWORDS = {explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ}
}

13

François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.

@Article{CDSJJB2016,
AUTHOR = {Chevenet, Fran{\~A}�ois and Doyon, Jean-Philippe and Scornavacca, Celine and Jacox, Edwin and Jousselin, Emmanuelle and Berry, Vincent},
TITLE = {SylvX: a viewer for phylogenetic tree reconciliations},
YEAR = {2016},
JOURNAL = {BIO},
VOLUME = {32},
NUMBER = {4},
PAGES = {608-610},
URL = {http://dx.doi.org/10.1093/bioinformatics/btv625},
NOTE = {https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization}
}

14

Jonathan Mitchell. Distinguishing Convergence on Phylogenetic Networks. PhD thesis, University of Tasmania, Australia, 2016.
Keywords: phylogenetic network, phylogeny, statistical model.
Note: http://arxiv.org/abs/1606.07160.

@PhdThesis{Mitchell2016,
AUTHOR = {Mitchell, Jonathan},
TITLE = {Distinguishing Convergence on Phylogenetic Networks},
YEAR = {2016},
SCHOOL = {University of Tasmania, Australia},
NOTE = {http://arxiv.org/abs/1606.07160},
KEYWORDS = {phylogenetic network, phylogeny, statistical model}
}

15

Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.

@Article{MathurAdlakha2016,
AUTHOR = {Mathur, Rinku and Adlakha, Neeru},
TITLE = {A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences},
YEAR = {2016},
JOURNAL = {Egyptian Journal of Basic and Applied Sciences},
VOLUME = {3},
NUMBER = {3},
PAGES = {263-271},
URL = {http://dx.doi.org/10.1016/j.ejbas.2016.07.004},
NOTE = {http://dx.doi.org/10.1016/j.ejbas.2016.07.004},
KEYWORDS = {from sequences, phylogenetic network, phylogeny, Program T REX}
}

16

Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016.
Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment.
Note: http://dx.doi.org/10.1093/bioinformatics/btw467.

@InProceedings{GLZ2016,
AUTHOR = {Gunawan, Andreas and Lu, Bingxin and Zhang, Louxin},
TITLE = {A program for verification of phylogenetic network models},
YEAR = {2016},
BOOKTITLE = {ECCB16},
VOLUME = {32},
NUMBER = {17},
PAGES = {i503-i510},
SERIES = {BIO},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btw467},
KEYWORDS = {exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment}
}

17

Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.

@Article{HejaseLiu2016,
AUTHOR = {Hejase, Hussein A. and Liu, Kevin J.},
TITLE = {A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation},
YEAR = {2016},
VOLUME = {17},
NUMBER = {422},
PAGES = {1-12},
URL = {http://dx.doi.org/10.1186/s12859-016-1277-1},
NOTE = {http://dx.doi.org/10.1186/s12859-016-1277-1},
KEYWORDS = {abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network}
}

18

Ioannis G. Tollis and Konstantinos G. Kakoulis. Algorithms for Visualizing Phylogenetic Networks. In GD16, Vol. 9801:183-195 of LNCS, springer, 2016.
Keywords: explicit network, galled network, galled tree, NP complete, planar, visualization.
Note: http://arxiv.org/abs/1609.00755.

@InProceedings{TollisKakoulis2016,
AUTHOR = {Tollis, Ioannis G. and Kakoulis, Konstantinos G.},
TITLE = {Algorithms for Visualizing Phylogenetic Networks},
YEAR = {2016},
BOOKTITLE = {GD16},
VOLUME = {9801},
PAGES = {183-195},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-50106-2_15},
NOTE = {http://arxiv.org/abs/1609.00755},
KEYWORDS = {explicit network, galled network, galled tree, NP complete, planar, visualization}
}

19

Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016.
Note: https://edoc.ub.uni-muenchen.de/19444/.

@PhdThesis{Albrecht2016,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing Hybridization Networks Using Agreement Forests},
YEAR = {2016},
SCHOOL = {Ludwig-Maximilians-Universit{\~A}�t M{\~A}�nchen},
NOTE = {https://edoc.ub.uni-muenchen.de/19444/}
}

20

Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016.
Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1607.06285.

@Article{GIKPS2016,
AUTHOR = {Gambette, Philippe and van Iersel, Leo and Kelk, Steven and Pardi, Fabio and Scornavacca, Celine},
TITLE = {Do branch lengths help to locate a tree in a phylogenetic network?},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {9},
PAGES = {1773-1795},
URL = {http://dx.doi.org/10.1007/s11538-016-0199-4},
NOTE = {http://arxiv.org/abs/1607.06285},
KEYWORDS = {branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network}
}

21

Nikita Alexeev and Max A. Alekseyev. Combinatorial Scoring of Phylogenetic Networks. In COCOON16, Vol. 9797:560-572 of LNCS, Springer, 2016.
Keywords: cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1602.02841.

@InProceedings{AlexeevAlekseyev2016,
AUTHOR = {Alexeev, Nikita and Alekseyev, Max A.},
TITLE = {Combinatorial Scoring of Phylogenetic Networks},
YEAR = {2016},
BOOKTITLE = {COCOON16},
VOLUME = {9797},
PAGES = {560-572},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-42634-1_45},
NOTE = {http://arxiv.org/abs/1602.02841},
KEYWORDS = {cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny}
}

22

Charles Semple. Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree. In BMB, Vol. 78(1):132-137, 2016.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.

@Article{Semple2016,
AUTHOR = {Semple, Charles},
TITLE = {Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {1},
PAGES = {132-137},
URL = {http://dx.doi.org/10.1007/s11538-015-0132-2},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network}
}

23

Katharina Huber, Vincent Moulton and Taoyang Wu. Transforming phylogenetic networks: Moving beyond tree space. In JTB, Vol. 404:30-39, 2016.
Keywords: distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1601.01788.

@Article{HMW2016,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Transforming phylogenetic networks: Moving beyond tree space},
YEAR = {2016},
JOURNAL = {JTB},
VOLUME = {404},
PAGES = {30-39},
URL = {http://dx.doi.org/10.1016/j.jtbi.2016.05.030},
NOTE = {http://arxiv.org/abs/1601.01788},
KEYWORDS = {distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny}
}

24

Maria Anaya, Olga Anipchenko-Ulaj, Aisha Ashfaq, Joyce Chiu, Mahedi Kaiser, Max Shoji Ohsawa, Megan Owen, Ella Pavlechko, Katherine St. John, Shivam Suleria, Keith Thompson and Corrine Yap. On Determining if Tree-based Networks Contain Fixed Trees. In BMB, Vol. 78(5):961-969, 2016.
Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1602.02739.

@Article{AAACKOOPSSTY2016,
AUTHOR = {Anaya, Maria and Anipchenko-Ulaj, Olga and Ashfaq, Aisha and Chiu, Joyce and Kaiser, Mahedi and Ohsawa, Max Shoji and Owen, Megan and Pavlechko, Ella and St. John, Katherine and Suleria, Shivam and Thompson, Keith and Yap, Corrine},
TITLE = {On Determining if Tree-based Networks Contain Fixed Trees},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {5},
PAGES = {961-969},
URL = {http://dx.doi.org/10.1007/s11538-016-0169-x},
NOTE = {http://arxiv.org/abs/1602.02739},
KEYWORDS = {explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network}
}

25

Momoko Hayamizu. On the existence of infinitely many universal tree-based networks. In JTB, Vol. 396:204-206, 2016.
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1512.02402.

@Article{Hayamizu2016,
AUTHOR = {Hayamizu, Momoko},
TITLE = {On the existence of infinitely many universal tree-based networks},
YEAR = {2016},
JOURNAL = {JTB},
VOLUME = {396},
PAGES = {204-206},
URL = {http://dx.doi.org/10.1016/j.jtbi.2016.02.023},
NOTE = {http://arxiv.org/abs/1512.02402},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, tree-based network}
}

26

Magnus Bordewich and Charles Semple. Determining phylogenetic networks from inter-taxa distances. In JOMB, Vol. 73(2):283-303, 2016.
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree-child network, uniqueness.
Note: http://132.181.26.35/~c.semple/papers/BS15b.pdf.

@Article{BordewichSemple2016,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Determining phylogenetic networks from inter-taxa distances},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {73},
NUMBER = {2},
PAGES = {283-303},
URL = {http://dx.doi.org/10.1007/s00285-015-0950-8},
NOTE = {http://132.181.26.35/~c.semple/papers/BS15b.pdf},
KEYWORDS = {from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree-child network, uniqueness}
}

27

James Oldman, Taoyang Wu, Leo van Iersel and Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):2151-2162, 2016.
Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.

@Article{OTIM2016,
AUTHOR = {Oldman, James and Wu, Taoyang and van Iersel, Leo and Moulton, Vincent},
TITLE = {TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories},
YEAR = {2016},
JOURNAL = {MBE},
VOLUME = {33},
NUMBER = {8},
PAGES = {2151-2162},
URL = {http://dx.doi.org/10.1093/molbev/msw068},
KEYWORDS = {explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction}
}

28

Dingqiao Wen, Yun Yu and Luay Nakhleh. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. In PLoS Genetics, Vol. 12(5):e1006006, 2016.
Keywords: bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.

@Article{WYL2016,
AUTHOR = {Wen, Dingqiao and Yu, Yun and Nakhleh, Luay},
TITLE = {Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent},
YEAR = {2016},
JOURNAL = {PLoS Genetics},
VOLUME = {12},
NUMBER = {5},
PAGES = {e1006006},
URL = {http://dx.doi.org/10.1371/journal.pgen.1006006},
KEYWORDS = {bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software}
}

29

Juan Wang. A Metric on the Space of Partly Reduced Phylogenetic Networks. In BMRI, Vol. 2016(7534258):1-9, 2016.
Keywords: distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks.
Note: http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf.

@Article{Wang2016,
AUTHOR = {Wang, Juan},
TITLE = {A Metric on the Space of Partly Reduced Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {BMRI},
VOLUME = {2016},
NUMBER = {7534258},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1155/2016/7534258},
NOTE = {http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf},
KEYWORDS = {distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks}
}

30

Jiafan Zhu, Yun Yu and Luay Nakhleh. In the Light of Deep Coalescence: Revisiting Trees Within Networks. In RECOMB-CG16, Vol. 17(suppl. 14):415.271-282 of BMCB, 2016.
Keywords: branch length, evaluation, explicit network, incomplete lineage sorting, phylogenetic network, phylogeny, statistical model, tree-based network, weakly displaying.
Note: http://arxiv.org/abs/1606.07350.

@InProceedings{ZYN2016,
AUTHOR = {Zhu, Jiafan and Yu, Yun and Nakhleh, Luay},
TITLE = {In the Light of Deep Coalescence: Revisiting Trees Within Networks},
YEAR = {2016},
BOOKTITLE = {RECOMB-CG16},
VOLUME = {17},
NUMBER = {suppl. 14},
PAGES = {415.271-282},
SERIES = {BMCB},
URL = {http://dx.doi.org/10.1186/s12859-016-1269-1},
NOTE = {http://arxiv.org/abs/1606.07350},
KEYWORDS = {branch length, evaluation, explicit network, incomplete lineage sorting, phylogenetic network, phylogeny, statistical model, tree-based network, weakly displaying}
}

31

Magnus Bordewich and Nihan Tokac. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. In DAM, Vol. 213:47-59, 2016.
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://dx.doi.org/10.1016/j.dam.2016.05.011.

@Article{BordewichTokac2016,
AUTHOR = {Bordewich, Magnus and Tokac, Nihan},
TITLE = {An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances},
YEAR = {2016},
JOURNAL = {DAM},
VOLUME = {213},
PAGES = {47-59},
URL = {http://dx.doi.org/10.1016/j.dam.2016.05.011},
NOTE = {http://dx.doi.org/10.1016/j.dam.2016.05.011},
KEYWORDS = {explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

32

Juan Wang, Zhang Zhibin and Yanjuan Li. Constructing phylogenetic networks based on the isomorphism of datasets. In BMRI, Vol. 2016(4236858):1-7, 2016.
Keywords: from clusters, phylogenetic network, phylogeny, reconstruction.
Note: http://downloads.hindawi.com/journals/bmri/aip/4236858.pdf.

@Article{WZL2016,
AUTHOR = {Wang, Juan and Zhibin, Zhang and Li, Yanjuan},
TITLE = {Constructing phylogenetic networks based on the isomorphism of datasets},
YEAR = {2016},
JOURNAL = {BMRI},
VOLUME = {2016},
NUMBER = {4236858},
PAGES = {1-7},
URL = {http://dx.doi.org/10.1155/2016/4236858},
NOTE = {http://downloads.hindawi.com/journals/bmri/aip/4236858.pdf},
KEYWORDS = {from clusters, phylogenetic network, phylogeny, reconstruction}
}

33

Dan Graur. Reticulate evolution and phylogenetic networks. In Molecular and Genome Evolution, Chapter 6, Sinauer, 2016.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf.

@InBook{Graur2016,
AUTHOR = {Graur, Dan},
TITLE = {Reticulate evolution and phylogenetic networks},
YEAR = {2016},
BOOKTITLE = {Molecular and Genome Evolution},
PUBLISHER = {Sinauer},
CHAPTER = {6},
NOTE = {http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf},
KEYWORDS = {phylogenetic network, phylogeny, survey}
}

34

Mike Steel. Introduction to phylogenetic networks. In Phylogeny: Discrete and Random Processes in Evolution, Vol. 89 of CBMS-NSF Regional Conference Series in Applied Mathematics, Chapter 10, SIAM, 2016.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
Note: http://bookstore.siam.org/cb89/.

@InBook{Steel2016,
AUTHOR = {Steel, Mike},
TITLE = {Introduction to phylogenetic networks},
YEAR = {2016},
BOOKTITLE = {Phylogeny: Discrete and Random Processes in Evolution},
VOLUME = {89},
SERIES = {CBMS-NSF Regional Conference Series in Applied Mathematics},
PUBLISHER = {SIAM},
CHAPTER = {10},
NOTE = {http://bookstore.siam.org/cb89/},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny, survey}
}

35

Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016.
Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey.
Note: http://dx.doi.org/10.1371/journal.pone.0165834.

@Article{Wang2016b,
AUTHOR = {Wang, Juan},
TITLE = {A Survey of Methods for Constructing Rooted Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {PLoS ONE},
VOLUME = {11},
NUMBER = {11},
PAGES = {e0165834},
URL = {http://dx.doi.org/10.1371/journal.pone.0165834},
NOTE = {http://dx.doi.org/10.1371/journal.pone.0165834},
KEYWORDS = {evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey}
}

36

Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016.
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://etheses.dur.ac.uk/11768/.

@PhdThesis{Tokac2016,
AUTHOR = {Tokac, Nihan},
TITLE = {Efficiency of Algorithms in Phylogenetics},
YEAR = {2016},
SCHOOL = {Durham University, U.K.},
URL = {http://etheses.dur.ac.uk/11768/},
NOTE = {http://etheses.dur.ac.uk/11768/},
KEYWORDS = {explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

37

Leo van Iersel, Steven Kelk and Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):1075-1089, 2016.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: https://arxiv.org/abs/1311.4045v3.

@Article{IKS2016,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Scornavacca, Celine},
TITLE = {Kernelizations for the hybridization number problem on multiple nonbinary trees},
YEAR = {2016},
JOURNAL = {JCSS},
VOLUME = {82},
NUMBER = {6},
PAGES = {1075-1089},
URL = {https://doi.org/10.1016/j.jcss.2016.03.006},
NOTE = {https://arxiv.org/abs/1311.4045v3},
KEYWORDS = {explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction}
}

38

Kristina Wicke. Extending the concept of phylogenetic diversity and its measures from trees to networks. Master's thesis, Ernst-Moritz-Arndt-Universität Greifswald, 2016.
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://math-inf.uni-greifswald.de/fileadmin/uni-greifswald/fakultaet/mnf/mathinf/wicke/MasterThesis_KristinaWicke.pdf.

@MastersThesis{Wicke2016,
AUTHOR = {Wicke, Kristina},
TITLE = {Extending the concept of phylogenetic diversity and its measures from trees to networks},
YEAR = {2016},
SCHOOL = {Ernst-Moritz-Arndt-Universit{\~A}�t Greifswald},
NOTE = {https://math-inf.uni-greifswald.de/fileadmin/uni-greifswald/fakultaet/mnf/mathinf/wicke/MasterThesis_KristinaWicke.pdf},
KEYWORDS = {diversity, explicit network, from network, normal network, phylogenetic network, phylogeny}
}

39

Edwin Jacox, Cédric Chauve, Gergely J. Szöllösi, Yann Ponty and Celine Scornavacca. EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony. In BIO, Vol. 32(13):2056-2058, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA.
Note: https://doi.org/10.1093/bioinformatics/btw105.

@Article{ECSPS2016,
AUTHOR = {Jacox, Edwin and Chauve, C{\~A}�dric and Sz{\~A}�ll{\~A}�si, Gergely J. and Ponty, Yann and Scornavacca, Celine},
TITLE = {EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony},
YEAR = {2016},
JOURNAL = {BIO},
VOLUME = {32},
NUMBER = {13},
PAGES = {2056-2058},
URL = {https://doi.org/10.1093/bioinformatics/btw105},
NOTE = {https://doi.org/10.1093/bioinformatics/btw105},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA}
}

40

Pei Wu. Quartet weights in phylogenetic network reconstruction. PhD thesis, University of Chinese Academy of Sciences, 2016.
Keywords: abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction.

@PhdThesis{Wu2016,
AUTHOR = {Wu, Pei},
TITLE = {Quartet weights in phylogenetic network reconstruction},
YEAR = {2016},
SCHOOL = {University of Chinese Academy of Sciences},
NOTE = {https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction},
KEYWORDS = {abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network}
}

41

Monika Balvociute. Flat Embeddings of Genetic and Distance Data. PhD thesis, University of Otago, 2016.
Keywords: abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network.
Note: http://hdl.handle.net/10523/6286.

@PhdThesis{Balvociute2016,
AUTHOR = {Balvociute, Monika},
TITLE = {Flat Embeddings of Genetic and Distance Data},
YEAR = {2016},
SCHOOL = {University of Otago},
URL = {http://hdl.handle.net/10523/6286},
NOTE = {http://hdl.handle.net/10523/6286},
KEYWORDS = {abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network}
}

42

Dingqiao Wen. Bayesian Inference of Phylogenetic Networks. Master's thesis, Rice University, Texas, 2016.
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1&isAllowed=y.

@MastersThesis{Wen2016,
AUTHOR = {Wen, Dingqiao},
TITLE = {Bayesian Inference of Phylogenetic Networks},
YEAR = {2016},
SCHOOL = {Rice University, Texas},
NOTE = {https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1{\&}isAllowed=y},
KEYWORDS = {bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}

2015

1

Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.

@Article{FIKS2015,
AUTHOR = {Fischer, Mareike and van Iersel, Leo and Kelk, Steven and Scornavacca, Celine},
TITLE = {On Computing The Maximum Parsimony Score Of A Phylogenetic Network},
YEAR = {2015},
JOURNAL = {SIDMA},
VOLUME = {29},
NUMBER = {1},
PAGES = {559-585},
URL = {http://dx.doi.org/10.1137/140959948},
NOTE = {http://arxiv.org/abs/1302.2430},
KEYWORDS = {APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software}
}

2

Colin McDiarmid, Charles Semple and Dominic Welsh. Counting phylogenetic networks. In Annals of Combinatorics, Vol. 19(1):205-224, 2015.
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/MSW13.pdf.

@Article{MSW2015,
AUTHOR = {McDiarmid, Colin and Semple, Charles and Welsh, Dominic},
TITLE = {Counting phylogenetic networks},
YEAR = {2015},
JOURNAL = {Annals of Combinatorics},
VOLUME = {19},
NUMBER = {1},
PAGES = {205-224},
URL = {http://dx.doi.org/10.1007/s00026-015-0260-2},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/MSW13.pdf},
KEYWORDS = {counting, explicit network, normal network, phylogenetic network, phylogeny, tree-child network}
}

3

Andrew R. Francis and Mike Steel. Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution? In MBIO, Vol. 259:12-19, 2015.
Keywords: from distances, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1405.2965.

@Article{FrancisSteel2015a,
AUTHOR = {Francis, Andrew R. and Steel, Mike},
TITLE = {Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution?},
YEAR = {2015},
JOURNAL = {MBIO},
VOLUME = {259},
PAGES = {12-19},
URL = {http://dx.doi.org/10.1016/j.mbs.2014.10.008},
NOTE = {http://arxiv.org/abs/1405.2965},
KEYWORDS = {from distances, phylogenetic network, phylogeny}
}

4

Katharina Huber, Leo van Iersel, Vincent Moulton and Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102-111, 2015.
Keywords: explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1093/sysbio/syu076.

@Article{HIMW2015,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Moulton, Vincent and Wu, Taoyang},
TITLE = {How much information is needed to infer reticulate evolutionary histories?},
YEAR = {2015},
JOURNAL = {Systematic Biology},
VOLUME = {64},
NUMBER = {1},
PAGES = {102-111},
URL = {http://dx.doi.org/10.1093/sysbio/syu076},
NOTE = {http://dx.doi.org/10.1093/sysbio/syu076},
KEYWORDS = {explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

5

Andrew R. Francis and Mike Steel. Which phylogenetic networks are merely trees with additional arcs? In Systematic Biology, Vol. 64(5):768-777, 2015.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, tree-based network.
Note: http://arxiv.org/abs/1502.07045.

@Article{FrancisSteel2015,
AUTHOR = {Francis, Andrew R. and Steel, Mike},
TITLE = {Which phylogenetic networks are merely trees with additional arcs?},
YEAR = {2015},
JOURNAL = {Systematic Biology},
VOLUME = {64},
NUMBER = {5},
PAGES = {768-777},
URL = {http://dx.doi.org/10.1093/sysbio/syv037},
NOTE = {http://arxiv.org/abs/1502.07045},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, polynomial, tree-based network}
}

6

Fabio Pardi and Celine Scornavacca. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable. In PLoS Computational Biology, Vol. 11(4):e1007137.1-23, 2015.
Keywords: branch length, explicit network, from rooted trees, identifiability, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pcbi.1004135.

@Article{PardiScornavacca2015,
AUTHOR = {Pardi, Fabio and Scornavacca, Celine},
TITLE = {Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable},
YEAR = {2015},
JOURNAL = {PLoS Computational Biology},
VOLUME = {11},
NUMBER = {4},
PAGES = {e1007137.1-23},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1004135},
NOTE = {http://dx.doi.org/10.1371/journal.pcbi.1004135},
KEYWORDS = {branch length, explicit network, from rooted trees, identifiability, phylogenetic network, phylogeny, reconstruction}
}

7

Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.

@InProceedings{GGLVZ2015,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}�phane and Zhang, Louxin},
TITLE = {Locating a Tree in A Phylogenetic Network in Quadratic Time},
YEAR = {2015},
BOOKTITLE = {RECOMB15},
VOLUME = {9029},
PAGES = {96-107},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-16706-0_12},
NOTE = {https://hal.archives-ouvertes.fr/hal-01116231/en},
KEYWORDS = {evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

8

Dan Gusfield. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach. In BCB15, Pages 443-451, 2015.
Keywords: explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1506.00678.

@InProceedings{Gusfield2015,
AUTHOR = {Gusfield, Dan},
TITLE = {Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach},
YEAR = {2015},
BOOKTITLE = {BCB15},
PAGES = {443-451},
URL = {http://dx.doi.org/10.1145/2808719.2808765},
NOTE = {http://arxiv.org/abs/1506.00678},
KEYWORDS = {explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction}
}

9

Quan Nguyen. Likelihood-based Phylogenetic Network Inference by Approximate Structural Expectation Maximization. Master's thesis, University of Helsinki, 2015.
Keywords: BIC, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://urn.fi/URN:NBN:fi-fe2015062910525.

@MastersThesis{Nguyen2015,
AUTHOR = {Nguyen, Quan},
TITLE = {Likelihood-based Phylogenetic Network Inference by Approximate Structural Expectation Maximization},
YEAR = {2015},
SCHOOL = {University of Helsinki},
URL = {http://urn.fi/URN:NBN:fi-fe2015062910525},
NOTE = {http://urn.fi/URN:NBN:fi-fe2015062910525},
KEYWORDS = {BIC, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software}
}

10

Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015.
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.

@InProceedings{NguyenRoos2015,
AUTHOR = {Nguyen, Quan and Roos, Teemu},
TITLE = {Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG},
YEAR = {2015},
BOOKTITLE = {AlCoB15},
VOLUME = {9199},
PAGES = {126-140},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-21233-3_10},
NOTE = {http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf},
KEYWORDS = {BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software}
}

11

Vladimir Ulyantsev and Mikhail Melnik. Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver. In AlCoB15, Vol. 9199:141-153 of LNCS, springer, 2015.
Keywords: explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
Note: https://www.researchgate.net/profile/Vladimir_Ulyantsev/publication/282816862_Constructing_Parsimonious_Hybridization_Networks_from_Multiple_Phylogenetic_Trees_Using_a_SAT-Solver/links/561d372c08aecade1acb3699/Constructing-Parsimonious-Hybridization-Networks-from-Multiple-Phylogenetic-Trees-Using-a-SAT-Solver.pdf.

@InProceedings{UlyantsevMelnik2015,
AUTHOR = {Ulyantsev, Vladimir and Melnik, Mikhail},
TITLE = {Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver},
YEAR = {2015},
BOOKTITLE = {AlCoB15},
VOLUME = {9199},
PAGES = {141-153},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-21233-3_11},
NOTE = {https://www.researchgate.net/profile/Vladimir_Ulyantsev/publication/282816862_Constructing_Parsimonious_Hybridization_Networks_from_Multiple_Phylogenetic_Trees_Using_a_SAT-Solver/links/561d372c08aecade1acb3699/Constructing-Parsimonious-Hybridization-Networks-from-Multiple-Phylogenetic-Trees-Using-a-SAT-Solver.pdf},
KEYWORDS = {explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction}
}

12

Jittat Fakcharoenphol, Tanee Kumpijit and Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337-342, IEEE, 2015.
Keywords: dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.

@InProceedings{FKP2015,
AUTHOR = {Fakcharoenphol, Jittat and Kumpijit, Tanee and Putwattana, Attakorn},
TITLE = {A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks},
YEAR = {2015},
BOOKTITLE = {Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15)},
PAGES = {337-342},
PUBLISHER = {IEEE},
URL = {http://dx.doi.org/10.1109/JCSSE.2015.7219820},
KEYWORDS = {dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

13

Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In ISBRA15, Vol. 9096:187-198 of LNCS, springer, 2015.
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf.

@InProceedings{KordiBansal2015,
AUTHOR = {Kordi, Misagh and Bansal, Mukul S.},
TITLE = {On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees},
YEAR = {2015},
BOOKTITLE = {ISBRA15},
VOLUME = {9096},
PAGES = {187-198},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-19048-8_16},
NOTE = {http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf},
KEYWORDS = {duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction}
}

14

Yun Yu and Luay Nakhleh. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378-389 of LNCS, springer, 2015.
Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf.

@InProceedings{YuNakhleh2015,
AUTHOR = {Yu, Yun and Nakhleh, Luay},
TITLE = {A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting},
YEAR = {2015},
BOOKTITLE = {ISBRA15},
VOLUME = {9096},
PAGES = {378-389},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-19048-8_32},
NOTE = {http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf},
KEYWORDS = {bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction}
}

15

Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. In BMCB, Vol. 16(236):1-15, 2015.
Keywords: agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0660-7.

@Article{Albrecht2015,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing all hybridization networks for multiple binary phylogenetic input trees},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {236},
PAGES = {1-15},
URL = {http://dx.doi.org/10.1186/s12859-015-0660-7},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0660-7},
KEYWORDS = {agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction}
}

16

Johannes Fischer and Daniel Peters. A Practical Succinct Data Structure for Tree-Like Graphs. In WALCOM15, Vol. 8973:65-76 of LNCS, springer, 2015.
Keywords: compression, from network, phylogenetic network, phylogeny.

@InProceedings{FischerPeters2015,
AUTHOR = {Fischer, Johannes and Peters, Daniel},
TITLE = {A Practical Succinct Data Structure for Tree-Like Graphs},
YEAR = {2015},
BOOKTITLE = {WALCOM15},
VOLUME = {8973},
PAGES = {65-76},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-15612-5_7},
KEYWORDS = {compression, from network, phylogenetic network, phylogeny}
}

17

Ward C Wheeler. Phylogenetic network analysis as a parsimony optimization problem. In BMCB, Vol. 16(296):1-9, 2015.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0675-0.

@Article{Wheeler2015,
AUTHOR = {Wheeler, Ward C},
TITLE = {Phylogenetic network analysis as a parsimony optimization problem},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {296},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1186/s12859-015-0675-0},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0675-0},
KEYWORDS = {explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction}
}

18

Maxime Morgado. Propriétés structurelles et relations des classes de réseaux phylogénétiques. Master's thesis, ENS Cachan, 2015.
Keywords: compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network.

@MastersThesis{Morgado2015,
AUTHOR = {Morgado, Maxime},
TITLE = {Propri{\~A}�t{\~A}�s structurelles et relations des classes de r{\~A}�seaux phylog{\~A}�n{\~A}�tiques},
YEAR = {2015},
SCHOOL = {ENS Cachan},
KEYWORDS = {compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network}
}

19

Yun Yu and Luay Nakhleh. A maximum pseudo-likelihood approach for phylogenetic networks. In RECOMB-CG15, Vol. 16(Suppl 10)(S10):1-10 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S10.

@InProceedings{YuNakhleh2015b,
AUTHOR = {Yu, Yun and Nakhleh, Luay},
TITLE = {A maximum pseudo-likelihood approach for phylogenetic networks},
YEAR = {2015},
BOOKTITLE = {RECOMB-CG15},
VOLUME = {16(Suppl 10)},
NUMBER = {S10},
PAGES = {1-10},
SERIES = {BMC Genomics},
PUBLISHER = {BioMed Central},
URL = {http://dx.doi.org/10.1186/1471-2164-16-S10-S10},
NOTE = {http://dx.doi.org/10.1186/1471-2164-16-S10-S10},
KEYWORDS = {explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance}
}

20

Sha Zhu, James H. Degnan, Sharyn J. Goldstein and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://dx.doi.org/10.1186/s12859-015-0721-y.

@Article{ZDGE2015,
AUTHOR = {Zhu, Sha and Degnan, James H. and Goldstein, Sharyn J. and Eldon, Bjarki},
TITLE = {Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {292},
PAGES = {1-7},
URL = {http://dx.doi.org/10.1186/s12859-015-0721-y},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0721-y},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software}
}

21

Gergely J. Szöllösi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin and Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 2015.
Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction.
Note: http://dx.doi.org/10.1098/rstb.2014.0335.

@Article{SDTDB2015,
AUTHOR = {Sz{\~A}�ll{\~A}�si, Gergely J. and Dav{\~A}�n, Adri{\~A}�n Arellano and Tannier, Eric and Daubin, Vincent and Boussau, Bastien},
TITLE = {Genome-scale phylogenetic analysis finds extensive gene transfer among fungi},
YEAR = {2015},
JOURNAL = {Philosophical Transactions of the Royal Society of London B: Biological Sciences},
VOLUME = {370},
NUMBER = {1678},
PAGES = {1-11},
URL = {http://dx.doi.org/10.1098/rstb.2014.0335},
NOTE = {http://dx.doi.org/10.1098/rstb.2014.0335},
KEYWORDS = {duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction}
}

22

Thu-Hien To and Celine Scornavacca. Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. In RECOMB-CG15, Vol. 16(Suppl 10)(S6):1-14 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S6.

@InProceedings{ToScornavacca2015,
AUTHOR = {To, Thu-Hien and Scornavacca, Celine},
TITLE = {Efficient algorithms for reconciling gene trees and species networks via duplication and loss events},
YEAR = {2015},
BOOKTITLE = {RECOMB-CG15},
VOLUME = {16(Suppl 10)},
NUMBER = {S6},
PAGES = {1-14},
SERIES = {BMC Genomics},
PUBLISHER = {BioMed Central},
URL = {http://dx.doi.org/10.1186/1471-2164-16-S10-S6},
NOTE = {http://dx.doi.org/10.1186/1471-2164-16-S10-S6},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction}
}

23

Dwueng-Chwuan Jhwueng and Brian O'Meara. Trait Evolution on Phylogenetic Networks. 2015.
Keywords: explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model.
Note: http://dx.doi.org/10.1101/023986.

@Misc{JhwuengOMeara2015,
AUTHOR = {Jhwueng, Dwueng-Chwuan and O'Meara, Brian},
TITLE = {Trait Evolution on Phylogenetic Networks},
YEAR = {2015},
URL = {http://dx.doi.org/10.1101/023986},
NOTE = {http://dx.doi.org/10.1101/023986},
KEYWORDS = {explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model}
}

24

Andreas Gunawan and Louxin Zhang. Bounding the Size of a Network Defined By Visibility Property. 2015.
Keywords: bound, explicit network, galled network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, stable-child network.
Note: http://arxiv.org/abs/1510.00115.

@Misc{GunawanZhang2015,
AUTHOR = {Gunawan, Andreas and Zhang, Louxin},
TITLE = {Bounding the Size of a Network Defined By Visibility Property},
YEAR = {2015},
NOTE = {http://arxiv.org/abs/1510.00115},
KEYWORDS = {bound, explicit network, galled network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, stable-child network}
}

25

Marc Thuillard and Didier Fraix-Burnet. Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers? In Evolutionary Bioinformatics, Vol. 11:213-221, 2015. [Abstract]
Keywords: circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split.
Note: http://dx.doi.org/10.4137%2FEBO.S28158.

@Article{ThuillardFraixBurnet2015,
AUTHOR = {Thuillard, Marc and Fraix-Burnet, Didier},
TITLE = {Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers?},
YEAR = {2015},
JOURNAL = {Evolutionary Bioinformatics},
VOLUME = {11},
PAGES = {213-221},
URL = {http://dx.doi.org/10.4137/EBO.S28158},
ABSTRACT = {This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters{\^a}�� approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.},
NOTE = {http://dx.doi.org/10.4137%2FEBO.S28158},
KEYWORDS = {circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split}
}

26

Laura Jetten. Characterising tree-based phylogenetic networks. Bachelor thesis, 2015.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://resolver.tudelft.nl/uuid:fda2636d-0ed5-4dd2-bacf-8abbbad8994e.

@Misc{Jetten2015,
AUTHOR = {Jetten, Laura},
TITLE = {Characterising tree-based phylogenetic networks},
YEAR = {2015},
HOWPUBLISHED = {Bachelor thesis},
NOTE = {http://resolver.tudelft.nl/uuid:fda2636d-0ed5-4dd2-bacf-8abbbad8994e},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network}
}

27

Benjamin Albrecht. Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests. 2015.
Keywords: agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05703.

@Misc{Albrecht2015a,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests},
YEAR = {2015},
NOTE = {http://arxiv.org/abs/1512.05703},
KEYWORDS = {agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software}
}

28

Benjamin Albrecht. Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees. 2015.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05656.

@Misc{Albrecht2015b,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees},
YEAR = {2015},
NOTE = {http://arxiv.org/abs/1512.05656},
KEYWORDS = {agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software}
}

29

Nela Lekic. Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks. PhD thesis, Maastricht University, The Netherlands, 2015.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.

@PhdThesis{Lekic2015,
AUTHOR = {Lekic, Nela},
TITLE = {Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks},
YEAR = {2015},
SCHOOL = {Maastricht University, The Netherlands},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction}
}

30

Jessica W. Leigh and David Bryant. PopART: full-feature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):1110-1116, 2015.
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.

@Article{LeighBryant2015,
AUTHOR = {Leigh, Jessica W. and Bryant, David},
TITLE = {PopART: full-feature software for haplotype network construction},
YEAR = {2015},
JOURNAL = {Methods in Ecology and Evolution},
VOLUME = {6},
NUMBER = {9},
PAGES = {1110-1116},
URL = {http://dx.doi.org/10.1111/2041-210X.12410},
NOTE = {http://dx.doi.org/10.1111/2041-210X.12410},
KEYWORDS = {abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software}
}

31

Gabriel Cardona, Joan Carles Pons and Francesc Rosselló. A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. In ALMOB, Vol. 10(28):1-15, 2015.
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network.
Note: http://dx.doi.org/10.1186/s13015-015-0059-z.

@Article{CPR2015,
AUTHOR = {Cardona, Gabriel and Pons, Joan Carles and Rossell{\~A}�, Francesc},
TITLE = {A reconstruction problem for a class of phylogenetic networks with lateral gene transfers},
YEAR = {2015},
JOURNAL = {ALMOB},
VOLUME = {10},
NUMBER = {28},
PAGES = {1-15},
URL = {http://dx.doi.org/10.1186/s13015-015-0059-z},
NOTE = {http://dx.doi.org/10.1186/s13015-015-0059-z},
KEYWORDS = {explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network}
}

32

Claudia Solís-Lemus. Statistical methods to infer population structure with coalescence and gene flow. PhD thesis, University of Wisconsin-Madison, 2015.
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network.
Note: https://www.stat.wisc.edu/~claudia/thesis.pdf.

@PhdThesis{SolisLemus2015,
AUTHOR = {Sol{\~A}�s-Lemus, Claudia},
TITLE = {Statistical methods to infer population structure with coalescence and gene flow},
YEAR = {2015},
SCHOOL = {University of Wisconsin-Madison},
NOTE = {https://www.stat.wisc.edu/~claudia/thesis.pdf},
KEYWORDS = {explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network}
}

2014

1

Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):49-66, 2014.
Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.3211.

Toggle abstract

@Article{IKLS2014,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Stougie, Leen},
TITLE = {Approximation algorithms for nonbinary agreement forests},
YEAR = {2014},
JOURNAL = {SIDMA},
VOLUME = {28},
NUMBER = {1},
PAGES = {49-66},
URL = {http://dx.doi.org/10.1137/120903567},
NOTE = {http://arxiv.org/abs/1210.3211},
KEYWORDS = {agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction}
}

2

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete. In The Scientific World Journal, Vol. 2014(254279):1-6, 2014.
Keywords: abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network.
Note: http://arxiv.org/abs/0902.4640.

Toggle abstract

@Article{CLRV2014,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete},
YEAR = {2014},
JOURNAL = {The Scientific World Journal},
VOLUME = {2014},
NUMBER = {254279},
PAGES = {1-6},
URL = {http://dx.doi.org/10.1155/2014/254279},
NOTE = {http://arxiv.org/abs/0902.4640},
KEYWORDS = {abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network}
}

3

Steven Kelk and Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886-915, 2014.
Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.3653.

Toggle abstract

@Article{KelkScornavacca2014,
AUTHOR = {Kelk, Steven and Scornavacca, Celine},
TITLE = {Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable},
YEAR = {2014},
JOURNAL = {ALG},
VOLUME = {68},
NUMBER = {4},
PAGES = {886-915},
URL = {http://dx.doi.org/10.1007/s00453-012-9708-5},
NOTE = {http://arxiv.org/abs/1108.3653},
KEYWORDS = {explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

4

Hadi Poormohammadi, Changiz Eslahchi and Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014.
Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1201.3722.

Toggle abstract

@Article{HCR2014,
AUTHOR = {Poormohammadi, Hadi and Eslahchi, Changiz and Tusserkani, Ruzbeh},
TITLE = {TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets},
YEAR = {2014},
JOURNAL = {PLoS ONE},
VOLUME = {9},
NUMBER = {9},
PAGES = {e106531},
URL = {http://dx.doi.org/10.1371/journal.pone.0106531},
NOTE = {http://arxiv.org/abs/1201.3722},
KEYWORDS = {explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software}
}

5

Sven Herrmann and Vincent Moulton. Computing the blocks of a quasi-median graph. In DAM, Vol. 179:129-138, 2014.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction.
Note: http://arxiv.org/abs/1206.6135.

@Article{HerrmannMoulton2014,
AUTHOR = {Herrmann, Sven and Moulton, Vincent},
TITLE = {Computing the blocks of a quasi-median graph},
YEAR = {2014},
JOURNAL = {DAM},
VOLUME = {179},
PAGES = {129-138},
URL = {http://dx.doi.org/10.1016/j.dam.2014.07.013},
NOTE = {http://arxiv.org/abs/1206.6135},
KEYWORDS = {abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction}
}

6

Leo van Iersel and Vincent Moulton. Trinets encode tree-child and level-2 phylogenetic networks. In JOMB, Vol. 68(7):1707-1729, 2014.
Keywords: explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.0362.

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@Article{IerselMoulton2014,
AUTHOR = {van Iersel, Leo and Moulton, Vincent},
TITLE = {Trinets encode tree-child and level-2 phylogenetic networks},
YEAR = {2014},
JOURNAL = {JOMB},
VOLUME = {68},
NUMBER = {7},
PAGES = {1707-1729},
URL = {http://dx.doi.org/10.1007/s00285-013-0683-5},
NOTE = {http://arxiv.org/abs/1210.0362},
KEYWORDS = {explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

7

Anthony Labarre and Sicco Verwer. Merging partially labelled trees: hardness and a declarative programming solution. In TCBB, Vol. 11(2):389-397, 2014.
Keywords: abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-00855669.

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@Article{LabarreVerwer2014,
AUTHOR = {Labarre, Anthony and Verwer, Sicco},
TITLE = {Merging partially labelled trees: hardness and a declarative programming solution},
YEAR = {2014},
JOURNAL = {TCBB},
VOLUME = {11},
NUMBER = {2},
PAGES = {389-397},
URL = {http://dx.doi.org/10.1109/TCBB.2014.2307200},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-00855669},
KEYWORDS = {abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction}
}

8

Judith Keijsper and Rudi Pendavingh. Reconstructing a phylogenetic level-1 network from quartets. In BMB, Vol. 76(10):2517-2541, 2014.
Keywords: explicit network, from quartets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1308.5206.

@Article{KeijsperPendavingh2014,
AUTHOR = {Keijsper, Judith and Pendavingh, Rudi},
TITLE = {Reconstructing a phylogenetic level-1 network from quartets},
YEAR = {2014},
JOURNAL = {BMB},
VOLUME = {76},
NUMBER = {10},
PAGES = {2517-2541},
URL = {http://dx.doi.org/10.1007/s11538-014-0022-z},
NOTE = {http://arxiv.org/abs/1308.5206},
KEYWORDS = {explicit network, from quartets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

9

Leo van Iersel and Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299-311 of LNCS, springer, 2014.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: http://arxiv.org/abs/1311.4045.

@InProceedings{IerselKelk2014,
AUTHOR = {van Iersel, Leo and Kelk, Steven},
TITLE = {Kernelizations for the hybridization number problem on multiple nonbinary trees},
YEAR = {2014},
BOOKTITLE = {WG14},
VOLUME = {8747},
PAGES = {299-311},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-12340-0_25},
NOTE = {http://arxiv.org/abs/1311.4045},
KEYWORDS = {explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction}
}

10

Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:66-78, 2014.
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.

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@Article{JanssonLingas2014,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2014},
JOURNAL = {Journal of Discrete Algorithms},
VOLUME = {25},
PAGES = {66-78},
URL = {http://dx.doi.org/10.1016/j.jda.2013.10.002},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance}
}

11

Ward C Wheeler. Phyletic groups on networks. In Cladistics, Vol. 30(4):447-451, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1111/cla.12062.

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@Article{Wheeler2014,
AUTHOR = {Wheeler, Ward C},
TITLE = {Phyletic groups on networks},
YEAR = {2014},
JOURNAL = {Cladistics},
VOLUME = {30},
NUMBER = {4},
PAGES = {447-451},
URL = {http://dx.doi.org/10.1111/cla.12062},
NOTE = {http://dx.doi.org/10.1111/cla.12062},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny}
}

12

Sarah Bastkowski, Andreas Spillner and Vincent Moulton. Fishing for minimum evolution trees with Neighbor-Nets. In IPL, Vol. 114(1-2):3-18, 2014.
Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.

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@Article{BSM2014,
AUTHOR = {Bastkowski, Sarah and Spillner, Andreas and Moulton, Vincent},
TITLE = {Fishing for minimum evolution trees with Neighbor-Nets},
YEAR = {2014},
JOURNAL = {IPL},
VOLUME = {114},
NUMBER = {1-2},
PAGES = {3-18},
URL = {http://dx.doi.org/10.1016/j.ipl.2013.10.003},
KEYWORDS = {circular split system, from distances, NeighborNet, phylogeny, polynomial}
}

13

Lavanya Kannan and Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303-319, 2014.
Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.

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@Article{KannanWheeler2014,
AUTHOR = {Kannan, Lavanya and Wheeler, Ward C},
TITLE = {Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming},
YEAR = {2014},
JOURNAL = {JCB},
VOLUME = {21},
NUMBER = {4},
PAGES = {303-319},
URL = {http://dx.doi.org/10.1089/cmb.2013.0134},
KEYWORDS = {explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction}
}

14

Jialiang Yang, Stefan Grünewald, Yifei Xu and Xiu-Feng Wan. Quartet-based methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1186/1752-0509-8-21 .

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@Article{YGXW2014,
AUTHOR = {Yang, Jialiang and Gr{\~A}�newald, Stefan and Xu, Yifei and Wan, Xiu-Feng},
TITLE = {Quartet-based methods to reconstruct phylogenetic networks},
YEAR = {2014},
JOURNAL = {BMC Systems Biology},
VOLUME = {80},
NUMBER = {21},
URL = {http://dx.doi.org/10.1186/1752-0509-8-21},
NOTE = {http://dx.doi.org/10.1186/1752-0509-8-21 },
KEYWORDS = {abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction}
}

15

Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal and Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87-i95 of BIO, 2014.
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btu289.

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@InProceedings{LWBK2014,
AUTHOR = {Libeskind-Hadas, Ran and Wu, Yi-Chieh and Bansal, Mukul S. and Kellis, Manolis},
TITLE = {Pareto-optimal phylogenetic tree reconciliation},
YEAR = {2014},
BOOKTITLE = {ISMB14},
VOLUME = {30},
PAGES = {i87-i95},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btu289},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btu289},
KEYWORDS = {duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction}
}

16

Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn and Luay Nakhleh. An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. In PLoS ONE, Vol. 10(6):e1003649, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM.
Note: http://arxiv.org/abs/1310.7989.

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@Article{LDTSKN2014,
AUTHOR = {Liu, Kevin J. and Dai, Jingxuan and Truong, Kathy and Song, Ying and Kohn, Michael H. and Nakhleh, Luay},
TITLE = {An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes},
YEAR = {2014},
JOURNAL = {PLoS ONE},
VOLUME = {10},
NUMBER = {6},
PAGES = {e1003649},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1003649},
NOTE = {http://arxiv.org/abs/1310.7989},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM}
}

17

David A. Morrison. Phylogenetic Networks: A Review of Methods to Display Evolutionary History. In Annual Research & Review in Biology, Vol. 4(10):1518-1543, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.

@Article{Morrison2014a,
AUTHOR = {Morrison, David A.},
TITLE = {Phylogenetic Networks: A Review of Methods to Display Evolutionary History},
YEAR = {2014},
JOURNAL = {Annual Research {\&} Review in Biology},
VOLUME = {4},
NUMBER = {10},
PAGES = {1518-1543},
URL = {https://dx.doi.org/10.9734/ARRB/2014/8230},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, reconstruction, survey}
}

18

David A. Morrison. Rooted Phylogenetic Networks for Exploratory Data Analysis. In Advances in Research, Vol. 2(3):145-152, 2014.
Keywords: abstract network, explicit network, phylogenetic network, reconstruction.

@Article{Morrison2014b,
AUTHOR = {Morrison, David A.},
TITLE = {Rooted Phylogenetic Networks for Exploratory Data Analysis},
YEAR = {2014},
JOURNAL = {Advances in Research},
VOLUME = {2},
NUMBER = {3},
PAGES = {145-152},
URL = {https://dx.doi.org/10.9734/AIR/2014/8485},
KEYWORDS = {abstract network, explicit network, phylogenetic network, reconstruction}
}

19

David A. Morrison. Next generation sequencing and phylogenetic networks. In EMBnet.journal, Vol. 20(e760):1-4, 2014.
Keywords: abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.

@Article{Morrison2014c,
AUTHOR = {Morrison, David A.},
TITLE = {Next generation sequencing and phylogenetic networks},
YEAR = {2014},
JOURNAL = {EMBnet.journal},
VOLUME = {20},
NUMBER = {e760},
PAGES = {1-4},
URL = {http://dx.doi.org/10.14806/ej.20.0.760},
KEYWORDS = {abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction}
}

20

Dan Gusfield. ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, 2014.
Keywords: ARG, explicit network, phylogenetic network, phylogeny, survey.
Note: http://mitpress.mit.edu/books/recombinatorics.